diff options
author | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-04-06 11:08:33 +0000 |
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committer | vrouvrea <vrouvrea@636b058d-ea47-450e-bf9e-a15bfbe3eedb> | 2016-04-06 11:08:33 +0000 |
commit | fb22bc9ca84f5b3c55a598bf0c903a73c117e783 (patch) | |
tree | e066a8a8fa5a07e2d0faf0be096cb542295def52 /src/Alpha_complex | |
parent | 3d592b82f837219ee9ecd8e33120563edb4e76ab (diff) |
Replace Delaunay_triangulation_off_io.h and Delaunay_triangulation_off_rw.cpp with
Points_off_io.h and CGAL_points_off_reader.cpp
Adapt UT and examples for this
Adapt Alpha complex for it
Alpha complex is now inserting points in a faster way (after a spatial_sort).
Remove Alpha complex construction from a pointer on Delaunay triangulation (no more needed).
Adapt documentation to all these modifications
Forbid copy/move constructor/assignment operator on Alpha complex
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alphashapes@1098 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 08a673b66451b5cb03fbdf482d696d93b35d220f
Diffstat (limited to 'src/Alpha_complex')
14 files changed, 247 insertions, 183 deletions
diff --git a/src/Alpha_complex/doc/Intro_alpha_complex.h b/src/Alpha_complex/doc/Intro_alpha_complex.h index 0dea2b16..9d0dcefa 100644 --- a/src/Alpha_complex/doc/Intro_alpha_complex.h +++ b/src/Alpha_complex/doc/Intro_alpha_complex.h @@ -112,14 +112,14 @@ namespace alphacomplex { * * \subsubsection dimension2 Dimension 2 * - * From the example above, it means the algorithm looks into each triangle ([4,2,1], [2,4,6], [4,5,6], ...), + * From the example above, it means the algorithm looks into each triangle ([0,1,2], [0,2,4], [1,2,3], ...), * computes the filtration value of the triangle, and then propagates the filtration value as described * here : - * \image html "alpha_complex_doc_421.png" "Filtration value propagation example" + * \image html "alpha_complex_doc_420.png" "Filtration value propagation example" * * \subsubsection dimension1 Dimension 1 * - * Then, the algorithm looks into each edge ([1,2], [4,2], [4,1], ...), + * Then, the algorithm looks into each edge ([0,1], [0,2], [1,2], ...), * computes the filtration value of the edge (in this case, propagation will have no effect). * * \subsubsection dimension0 Dimension 0 diff --git a/src/Alpha_complex/doc/alpha_complex_doc.ipe b/src/Alpha_complex/doc/alpha_complex_doc.ipe index 99bd05af..baf0d26a 100644 --- a/src/Alpha_complex/doc/alpha_complex_doc.ipe +++ b/src/Alpha_complex/doc/alpha_complex_doc.ipe @@ -1,7 +1,7 @@ <?xml version="1.0"?> <!DOCTYPE ipe SYSTEM "ipe.dtd"> <ipe version="70107" creator="Ipe 7.1.10"> -<info created="D:20150603143945" modified="D:20160315144626"/> +<info created="D:20150603143945" modified="D:20160406112209"/> <ipestyle name="basic"> <symbol name="arrow/arc(spx)"> <path stroke="sym-stroke" fill="sym-stroke" pen="sym-pen"> @@ -253,13 +253,13 @@ h 320 580 l </path> <text matrix="1 0 0 1 -260 0" transformations="translations" pos="380 530" stroke="darkcyan" type="label" width="118.196" height="8.307" depth="2.32" valign="baseline" size="large">Delaunay triangulation</text> -<text 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+</path> </page> </ipe> diff --git a/src/Alpha_complex/doc/alpha_complex_doc.png b/src/Alpha_complex/doc/alpha_complex_doc.png Binary files differindex cfe3ede6..0b6201da 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_421.ipe b/src/Alpha_complex/doc/alpha_complex_doc_420.ipe index 727816c5..5d1d29d4 100644 --- a/src/Alpha_complex/doc/alpha_complex_doc_421.ipe +++ b/src/Alpha_complex/doc/alpha_complex_doc_420.ipe @@ -252,14 +252,14 @@ h 350 520 l 320 580 l </path> -<text matrix="1 0 0 1 0 80" transformations="translations" pos="380 530" stroke="darkcyan" type="label" width="54.628" height="8.965" depth="2.99" valign="baseline" size="large">Cell [4,2,1]</text> -<text matrix="1 0 0 1 -2.15463 76.4987" transformations="translations" pos="282.952 524.893" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">2</text> -<text matrix="1 0 0 1 0 80" 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transformations="translations" pos="272.179 660.635" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">4</text> +<text matrix="1 0 0 1 0.700256 69.8463" transformations="translations" pos="296.419 724.197" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">5</text> +<text matrix="1 0 0 1 0 80" transformations="translations" pos="375.332 689.453" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">6</text> <path matrix="1 0 0 1 0 80" stroke="lightgray"> 280 660 m 300 710 l @@ -285,7 +285,7 @@ h 243.428 591.569 m 186.061 643.28 l </path> -<text matrix="1 0 0 1 0 80" transformations="translations" pos="212.724 627.389" stroke="darkcyan" type="label" width="18.785" height="4.294" depth="1.49" valign="baseline">$\alpha_{421}$</text> +<text matrix="1 0 0 1 0 80" transformations="translations" pos="212.724 627.389" stroke="darkcyan" type="label" width="18.785" height="4.294" depth="1.49" valign="baseline">$\alpha_{420}$</text> <path matrix="1 0 0 1 -264 -162" stroke="lightgray"> 320 580 m 350 520 l @@ -306,15 +306,15 @@ h 350 520 l 320 580 l </path> -<text matrix="0.582962 0 0 1 -211.265 -209.555" transformations="translations" pos="380 530" stroke="darkcyan" type="label" width="231.798" height="8.965" depth="2.99" valign="baseline" size="large">[4,2] is Gabriel $\rightarrow$ $\alpha_{42}$ is not$\\$ +<text matrix="0.582962 0 0 1 -211.265 -209.555" transformations="translations" pos="380 530" stroke="darkcyan" type="label" width="231.798" height="8.965" depth="2.99" valign="baseline" size="large">[2,0] is Gabriel $\rightarrow$ $\alpha_{20}$ is not$\\$ modified (NaN) </text> -<text matrix="1 0 0 1 -266.155 -165.501" transformations="translations" pos="282.952 524.893" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">2</text> -<text matrix="1 0 0 1 -264 -162" transformations="translations" pos="310.693 578.759" stroke="black" 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matrix="1 0 0 1 -264 -162" transformations="translations" pos="310.693 578.759" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">2</text> +<text matrix="1 0 0 1 -264 -162" transformations="translations" pos="375.332 578.49" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">3</text> +<text matrix="1 0 0 1 -264 -172" transformations="translations" pos="272.179 660.635" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">4</text> +<text matrix="1 0 0 1 -263.3 -172.154" transformations="translations" pos="296.419 724.197" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">5</text> +<text matrix="1 0 0 1 -264 -162" transformations="translations" pos="375.332 689.453" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">6</text> <path matrix="1 0 0 1 -264 -162" stroke="lightgray"> 280 660 m 300 710 l @@ -333,7 +333,7 @@ modified 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height="6.42" depth="0" valign="baseline">2</text> -<text matrix="1 0 0 1 -38 -164" transformations="translations" pos="375.332 578.49" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">5</text> -<text matrix="1 0 0 1 -37.2997 -174.154" transformations="translations" pos="296.419 724.197" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">3</text> -<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">0</text> +<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">[0,4] is not Gabriel $\rightarrow$ $\alpha_{40} = \alpha_{420}$</text> +<text matrix="1 0 0 1 -40.1546 -167.501" transformations="translations" pos="282.952 524.893" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">0</text> +<text matrix="1 0 0 1 -38 -164" transformations="translations" pos="375.332 578.49" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">3</text> +<text matrix="1 0 0 1 -37.2997 -174.154" transformations="translations" pos="296.419 724.197" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">5</text> +<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">6</text> <path matrix="1 0 0 1 -38 -164" stroke="lightgray"> 280 660 m 300 710 l @@ -388,7 +388,7 @@ modified (NaN) 320 580 l 280 660 l </path> -<text matrix="1 0 0 1 52.4654 -193.97" transformations="translations" pos="212.724 627.389" stroke="darkcyan" type="label" width="14.814" height="4.294" depth="1.49" valign="baseline">$\alpha_{12}$</text> +<text matrix="1 0 0 1 52.4654 -193.97" transformations="translations" pos="212.724 627.389" stroke="darkcyan" type="label" width="14.814" height="4.294" depth="1.49" valign="baseline">$\alpha_{40}$</text> <path matrix="1 0 0 1 -38 -164" stroke="darkcyan" pen="heavier"> 290 530 m 280 660 l @@ -413,12 +413,12 @@ modified (NaN) 350 520 l 320 580 l </path> -<text matrix="1 0 0 1 123.845 -165.501" transformations="translations" pos="282.952 524.893" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">2</text> -<text matrix="1 0 0 1 126 -162" transformations="translations" pos="352.708 510.349" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">6</text> -<text matrix="1 0 0 1 126 -162" transformations="translations" pos="310.693 578.759" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">4</text> -<text matrix="1 0 0 1 126 -162" transformations="translations" pos="375.332 578.49" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">5</text> -<text matrix="1 0 0 1 126.7 -172.154" transformations="translations" pos="296.419 724.197" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">3</text> -<text matrix="1 0 0 1 126 -162" transformations="translations" pos="375.332 689.453" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">0</text> +<text matrix="1 0 0 1 123.845 -165.501" transformations="translations" pos="282.952 524.893" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">0</text> +<text matrix="1 0 0 1 126 -162" transformations="translations" pos="352.708 510.349" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">1</text> +<text matrix="1 0 0 1 126 -162" transformations="translations" pos="310.693 578.759" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">2</text> +<text matrix="1 0 0 1 126 -162" transformations="translations" pos="375.332 578.49" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">3</text> +<text matrix="1 0 0 1 126.7 -172.154" transformations="translations" pos="296.419 724.197" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">5</text> +<text matrix="1 0 0 1 126 -162" transformations="translations" pos="375.332 689.453" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">6</text> <path matrix="1 0 0 1 126 -162" stroke="lightgray"> 280 660 m 300 710 l @@ -437,8 +437,8 @@ modified (NaN) 320 580 l 280 660 l </path> -<text matrix="1 0 0 1 225.859 -165.729" transformations="translations" pos="212.724 627.389" stroke="darkcyan" type="label" width="14.814" height="4.294" depth="1.49" valign="baseline">$\alpha_{41}$</text> -<text matrix="1 0 0 1 122 -164" transformations="translations" pos="272.179 660.635" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">1</text> +<text matrix="1 0 0 1 225.859 -165.729" transformations="translations" pos="212.724 627.389" stroke="darkcyan" type="label" width="14.814" height="4.294" depth="1.49" valign="baseline">$\alpha_{42}$</text> +<text matrix="1 0 0 1 122 -164" transformations="translations" pos="272.179 660.635" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">4</text> <path stroke="darkcyan" pen="heavier"> 406.093 497.775 m 446.094 418.092 l @@ -450,7 +450,7 @@ modified (NaN) 425.854 457.774 m 470.795 457.774 l </path> -<text matrix="1 0 0 1 -48.9756 -209.799" transformations="translations" pos="380 530" stroke="darkcyan" type="label" width="231.798" height="8.965" depth="2.99" valign="baseline" size="large">[4,1] is Gabriel $\rightarrow$ $\alpha_{41}$ is not modified (NaN) +<text matrix="1 0 0 1 -48.9756 -209.799" transformations="translations" pos="380 530" stroke="darkcyan" type="label" width="231.798" height="8.965" depth="2.99" valign="baseline" size="large">[2,4] is Gabriel $\rightarrow$ $\alpha_{42}$ is not modified (NaN) </text> <path stroke="darkblue" arrow="normal/normal"> 205.028 596.091 m @@ -464,9 +464,9 @@ modified (NaN) 341.123 594.316 m 413.904 554.079 l </path> -<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 [4,2,1]</text> +<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 [4,2,0]</text> <text matrix="1 0 0 1 -93.391 2.68003" transformations="translations" pos="104.437 300.174" stroke="black" type="label" width="208.621" height="6.926" depth="1.93" valign="baseline">N.B. : is Gabriel on a single point has no sense.</text> -<text matrix="1 0 0 1 -36.9231 10" transformations="translations" pos="48 784" stroke="black" type="label" width="118.324" height="7.473" depth="2.49" valign="baseline">Dimension =2 - $\sigma$ = [4,2,1]</text> +<text matrix="1 0 0 1 -36.9231 10" transformations="translations" pos="48 784" stroke="black" type="label" width="118.324" height="7.473" depth="2.49" valign="baseline">Dimension =2 - $\sigma$ = [4,2,0]</text> <path stroke="darkcyan"> 247.333 430.892 m 311.764 430.892 l @@ -484,19 +484,19 @@ modified (NaN) <use matrix="1 0 0 1 -264 -162" name="mark/fdisk(sfx)" pos="370 690" size="normal" stroke="black" fill="white"/> <use matrix="1 0 0 1 -264 -162" name="mark/fdisk(sfx)" pos="370 580" size="normal" stroke="black" fill="white"/> <use matrix="1 0 0 1 -264 -162" name="mark/fdisk(sfx)" pos="350 520" size="normal" stroke="black" fill="white"/> -<text matrix="1 0 0 1 -264 -162" transformations="translations" pos="352.708 510.349" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">6</text> +<text matrix="1 0 0 1 -264 -162" transformations="translations" pos="352.708 510.349" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">1</text> <use matrix="1 0 0 1 -264 -162" name="mark/fdisk(sfx)" pos="305 555" size="normal" stroke="darkcyan" fill="white"/> <use matrix="1 0 0 1 -264 -162" name="mark/fdisk(sfx)" pos="290 530" size="normal" stroke="black" fill="white"/> <use matrix="1 0 0 1 -264 -162" name="mark/fdisk(sfx)" pos="320 580" size="normal" stroke="black" fill="white"/> <use matrix="1 0 0 1 -37.2997 -174.154" name="mark/fdisk(sfx)" pos="300 720" size="normal" stroke="black" fill="white"/> <use matrix="1 0 0 1 -38 -164" name="mark/fdisk(sfx)" pos="370 690" size="normal" stroke="black" fill="white"/> -<text matrix="1 0 0 1 -38 -164" transformations="translations" pos="272.179 660.635" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">1</text> +<text matrix="1 0 0 1 -38 -164" transformations="translations" pos="272.179 660.635" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">4</text> <use name="mark/fdisk(sfx)" pos="247 431" size="normal" stroke="darkcyan" fill="white"/> <use matrix="1 0 0 1 -38 -164" name="mark/fdisk(sfx)" pos="350 520" size="normal" stroke="black" fill="white"/> -<text matrix="1 0 0 1 -38 -164" transformations="translations" pos="352.708 510.349" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">6</text> +<text matrix="1 0 0 1 -38 -164" transformations="translations" pos="352.708 510.349" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">1</text> <use matrix="1 0 0 1 -38 -164" name="mark/fdisk(sfx)" pos="370 580" size="normal" stroke="black" fill="white"/> <use matrix="1 0 0 1 -38 -164" name="mark/fdisk(sfx)" pos="320 580" size="normal" stroke="darkred" fill="white"/> -<text matrix="1 0 0 1 -38 -164" transformations="translations" pos="310.693 578.759" stroke="darkred" type="label" width="4.981" height="6.42" depth="0" valign="baseline">4</text> +<text matrix="1 0 0 1 -38 -164" transformations="translations" pos="310.693 578.759" stroke="darkred" type="label" width="4.981" height="6.42" depth="0" valign="baseline">2</text> <path matrix="1 0 0 1 -38 -164" stroke="darkred" pen="heavier"> 65.192 0 0 65.192 285 595 e </path> diff --git a/src/Alpha_complex/doc/alpha_complex_doc_420.png b/src/Alpha_complex/doc/alpha_complex_doc_420.png Binary files differnew file mode 100644 index 00000000..ef7187f7 --- /dev/null +++ b/src/Alpha_complex/doc/alpha_complex_doc_420.png diff --git a/src/Alpha_complex/doc/alpha_complex_doc_421.png b/src/Alpha_complex/doc/alpha_complex_doc_421.png Binary files differdeleted file mode 100644 index 1cce4402..00000000 --- a/src/Alpha_complex/doc/alpha_complex_doc_421.png +++ /dev/null diff --git a/src/Alpha_complex/doc/alpha_complex_representation.ipe b/src/Alpha_complex/doc/alpha_complex_representation.ipe index fead1661..e8096b93 100644 --- a/src/Alpha_complex/doc/alpha_complex_representation.ipe +++ b/src/Alpha_complex/doc/alpha_complex_representation.ipe @@ -1,7 +1,7 @@ <?xml version="1.0"?> <!DOCTYPE ipe SYSTEM "ipe.dtd"> <ipe version="70107" creator="Ipe 7.1.10"> -<info created="D:20150603143945" modified="D:20151127174742"/> +<info created="D:20150603143945" modified="D:20160404172133"/> <ipestyle name="basic"> <symbol name="arrow/arc(spx)"> <path stroke="sym-stroke" fill="sym-stroke" pen="sym-pen"> @@ -251,13 +251,13 @@ h h </path> <text matrix="1 0 0 1 -230.178 22.1775" transformations="translations" pos="380 530" stroke="seagreen" type="label" width="76.735" height="8.307" depth="2.32" valign="baseline" size="large">Alpha complex</text> -<text matrix="1 0 0 1 -212.333 18.6762" transformations="translations" pos="282.952 524.893" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">2</text> -<text matrix="1 0 0 1 -210.178 22.1775" transformations="translations" pos="352.708 510.349" 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valign="baseline">0</text> +<text matrix="1 0 0 1 -212.333 18.6762" transformations="translations" pos="282.952 524.893" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">0</text> +<text matrix="1 0 0 1 -210.178 22.1775" transformations="translations" pos="352.708 510.349" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">1</text> +<text matrix="1 0 0 1 -210.178 22.1775" transformations="translations" pos="310.693 578.759" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">2</text> +<text matrix="1 0 0 1 -210.178 22.1775" transformations="translations" pos="375.332 578.49" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">3</text> +<text matrix="1 0 0 1 -210.178 22.1775" transformations="translations" pos="272.179 660.635" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">4</text> +<text matrix="1 0 0 1 -209.478 12.0238" transformations="translations" pos="296.419 724.197" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">5</text> +<text matrix="1 0 0 1 -210.178 22.1775" transformations="translations" pos="375.332 689.453" stroke="black" type="label" width="4.981" height="6.42" depth="0" valign="baseline">6</text> <path matrix="1 0 0 1 31.9779 -58.7483" stroke="darkgray"> 58.1341 0 0 58.1341 218.925 692.601 e </path> diff --git a/src/Alpha_complex/doc/alpha_complex_representation.png b/src/Alpha_complex/doc/alpha_complex_representation.png Binary files differindex 9833bff3..7b81cd69 100644 --- a/src/Alpha_complex/doc/alpha_complex_representation.png +++ b/src/Alpha_complex/doc/alpha_complex_representation.png diff --git a/src/Alpha_complex/example/Alpha_complex_from_off.cpp b/src/Alpha_complex/example/Alpha_complex_from_off.cpp index 18a1a20d..963ef5ca 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_off.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_off.cpp @@ -4,17 +4,15 @@ #include <iostream> #include <string> -void usage(char * const progName) { +void usage(int nbArgs, char * const progName) { + std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; std::cerr << "Usage: " << progName << " filename.off alpha_square_max_value [ouput_file.txt]\n"; std::cerr << " i.e.: " << progName << " ../../data/points/alphacomplexdoc.off 60.0\n"; exit(-1); // ----- >> } int main(int argc, char **argv) { - if ((argc != 3) && (argc != 4)) { - std::cerr << "Error: Number of arguments (" << argc << ") is not correct\n"; - usage(argv[0]); - } + if ((argc != 3) && (argc != 4)) usage(argc, (argv[0] - 1)); std::string off_file_name(argv[1]); double alpha_square_max_value = atof(argv[2]); diff --git a/src/Alpha_complex/example/Alpha_complex_from_points.cpp b/src/Alpha_complex/example/Alpha_complex_from_points.cpp index 815e40d7..cd17af1e 100644 --- a/src/Alpha_complex/example/Alpha_complex_from_points.cpp +++ b/src/Alpha_complex/example/Alpha_complex_from_points.cpp @@ -4,13 +4,26 @@ #include <iostream> #include <string> #include <vector> +#include <limits> // for numeric limits typedef CGAL::Epick_d< CGAL::Dimension_tag<2> > Kernel; typedef Kernel::Point_d Point; typedef std::vector<Point> Vector_of_points; +void usage(int nbArgs, char * const progName) { + std::cerr << "Error: Number of arguments (" << nbArgs << ") is not correct\n"; + std::cerr << "Usage: " << progName << " [alpha_square_max_value]\n"; + std::cerr << " i.e.: " << progName << " 60.0\n"; + exit(-1); // ----- >> +} + int main(int argc, char **argv) { - double alpha_square_max_value = 60.0; + if ((argc != 1) && (argc != 2)) usage(argc, (argv[0] - 1)); + + // Delaunay complex if alpha_square_max_value is not given by the user. + double alpha_square_max_value = std::numeric_limits<double>::infinity(); + if (argc == 2) + alpha_square_max_value = atof(argv[1]); // ---------------------------------------------------------------------------- // Init of a list of points diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt index 5869fdff..13183e86 100644 --- a/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt +++ b/src/Alpha_complex/example/alphaoffreader_for_doc_32.txt @@ -7,16 +7,16 @@ Iterator on alpha complex simplices in the filtration order, with [filtration va ( 4 ) -> [0] ( 5 ) -> [0] ( 6 ) -> [0] - ( 5 4 ) -> [6.25] - ( 3 1 ) -> [7.25] - ( 4 2 ) -> [8.5] - ( 6 2 ) -> [9.25] - ( 6 5 ) -> [10] - ( 6 4 ) -> [11.25] - ( 6 5 4 ) -> [12.5] - ( 6 4 2 ) -> [12.9959] - ( 3 0 ) -> [13.25] - ( 4 1 ) -> [20] - ( 1 0 ) -> [22.7367] - ( 3 1 0 ) -> [22.7367] - ( 5 0 ) -> [30.25] + ( 3 2 ) -> [6.25] + ( 5 4 ) -> [7.25] + ( 2 0 ) -> [8.5] + ( 1 0 ) -> [9.25] + ( 3 1 ) -> [10] + ( 2 1 ) -> [11.25] + ( 3 2 1 ) -> [12.5] + ( 2 1 0 ) -> [12.9959] + ( 6 5 ) -> [13.25] + ( 4 2 ) -> [20] + ( 6 4 ) -> [22.7367] + ( 6 5 4 ) -> [22.7367] + ( 6 3 ) -> [30.25] diff --git a/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt index 1d17a58a..71f29a00 100644 --- a/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt +++ b/src/Alpha_complex/example/alphaoffreader_for_doc_60.txt @@ -7,21 +7,21 @@ Iterator on alpha complex simplices in the filtration order, with [filtration va ( 4 ) -> [0] ( 5 ) -> [0] ( 6 ) -> [0] - ( 5 4 ) -> [6.25] - ( 3 1 ) -> [7.25] - ( 4 2 ) -> [8.5] - ( 6 2 ) -> [9.25] - ( 6 5 ) -> [10] - ( 6 4 ) -> [11.25] - ( 6 5 4 ) -> [12.5] - ( 6 4 2 ) -> [12.9959] - ( 3 0 ) -> [13.25] - ( 4 1 ) -> [20] - ( 1 0 ) -> [22.7367] - ( 3 1 0 ) -> [22.7367] - ( 5 0 ) -> [30.25] - ( 4 0 ) -> [36.5] - ( 5 4 0 ) -> [36.5] - ( 4 1 0 ) -> [37.2449] - ( 2 1 ) -> [59.7107] - ( 4 2 1 ) -> [59.7107] + ( 3 2 ) -> [6.25] + ( 5 4 ) -> [7.25] + ( 2 0 ) -> [8.5] + ( 1 0 ) -> [9.25] + ( 3 1 ) -> [10] + ( 2 1 ) -> [11.25] + ( 3 2 1 ) -> [12.5] + ( 2 1 0 ) -> [12.9959] + ( 6 5 ) -> [13.25] + ( 4 2 ) -> [20] + ( 6 4 ) -> [22.7367] + ( 6 5 4 ) -> [22.7367] + ( 6 3 ) -> [30.25] + ( 6 2 ) -> [36.5] + ( 6 3 2 ) -> [36.5] + ( 6 4 2 ) -> [37.2449] + ( 4 0 ) -> [59.7107] + ( 4 2 0 ) -> [59.7107] diff --git a/src/Alpha_complex/include/gudhi/Alpha_complex.h b/src/Alpha_complex/include/gudhi/Alpha_complex.h index 2b27a459..21eb5f48 100644 --- a/src/Alpha_complex/include/gudhi/Alpha_complex.h +++ b/src/Alpha_complex/include/gudhi/Alpha_complex.h @@ -27,14 +27,16 @@ #include <gudhi/graph_simplicial_complex.h> #include <gudhi/Simplex_tree.h> #include <gudhi/Debug_utils.h> -// to construct a Delaunay_triangulation from a OFF file -#include <gudhi/Delaunay_triangulation_off_io.h> +// to construct Alpha_complex from a OFF file of points +#include <gudhi/Points_off_io.h> #include <stdlib.h> #include <math.h> // isnan, fmax +//#include <CGAL/Triangulation_data_structure.h> #include <CGAL/Delaunay_triangulation.h> #include <CGAL/Epick_d.h> +#include <CGAL/Spatial_sort_traits_adapter_d.h> #include <iostream> #include <vector> @@ -43,6 +45,7 @@ #include <map> #include <utility> // std::pair #include <stdexcept> +#include <numeric> // for std::iota namespace Gudhi { @@ -57,7 +60,7 @@ namespace alphacomplex { * \details * The data structure can be constructed from a CGAL Delaunay triangulation (for more informations on CGAL Delaunay * triangulation, please refer to the corresponding chapter in page http://doc.cgal.org/latest/Triangulation/) or from - * an OFF file (cf. Delaunay_triangulation_off_reader). + * an OFF file (cf. Points_off_reader). * * Please refer to \ref alpha_complex for examples. * @@ -74,13 +77,19 @@ namespace alphacomplex { template<class Kernel = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>> class Alpha_complex : public Simplex_tree<> { public: + // Add an int in TDS to save point index in the structure + typedef CGAL::Triangulation_data_structure<CGAL::Dynamic_dimension_tag, + CGAL::Triangulation_vertex<Kernel, int>, + CGAL::Triangulation_full_cell<Kernel> > TDS; /** \brief A Delaunay triangulation of a set of points in \f$ \mathbb{R}^D\f$.*/ - typedef typename CGAL::Delaunay_triangulation<Kernel> Delaunay_triangulation; + typedef CGAL::Delaunay_triangulation<Kernel, TDS> Delaunay_triangulation; + /** \brief A point in Euclidean space.*/ typedef typename Kernel::Point_d Point_d; /** \brief Geometric traits class that provides the geometric types and predicates needed by Delaunay * triangulations.*/ typedef Kernel Geom_traits; + private: // From Simplex_tree // Type required to insert into a simplex_tree (with or without subfaces). @@ -104,7 +113,7 @@ class Alpha_complex : public Simplex_tree<> { // Double map type to switch from CGAL vertex iterator to simplex tree vertex handle and vice versa. typedef typename std::map< CGAL_vertex_iterator, Vertex_handle > Map_vertex_iterator_to_handle; - typedef typename std::vector< CGAL_vertex_iterator > Vector_vertex_iterator; + typedef typename std::map< Vertex_handle, CGAL_vertex_iterator > Vector_vertex_iterator; private: /** \brief Map to switch from CGAL vertex iterator to simplex tree vertex handle.*/ @@ -128,28 +137,13 @@ class Alpha_complex : public Simplex_tree<> { Alpha_complex(const std::string& off_file_name, Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity()) : triangulation_(nullptr) { - Gudhi::Delaunay_triangulation_off_reader<Delaunay_triangulation> off_reader(off_file_name); + Gudhi::Points_off_reader<Point_d> off_reader(off_file_name); if (!off_reader.is_valid()) { std::cerr << "Alpha_complex - Unable to read file " << off_file_name << "\n"; exit(-1); // ----- >> } - triangulation_ = off_reader.get_complex(); - init(max_alpha_square); - } - /** \brief Alpha_complex constructor from a Delaunay triangulation. - * - * @param[in] triangulation_ptr Pointer on a <a target="_blank" - * href="http://doc.cgal.org/latest/Triangulation/index.html#Chapter_Triangulations"> - * CGAL::Delaunay_triangulation<Kernel></a> \cite cgal:hdj-t-15b. - * Alpha_complex takes ownership of the Delaunay_triangulation object, which must have been allocated using operator - * new. - * @param[in] max_alpha_square maximum for alpha square value. Default value is +\f$\infty\f$. - */ - Alpha_complex(Delaunay_triangulation* triangulation_ptr, - Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity()) - : triangulation_(triangulation_ptr) { - init(max_alpha_square); + init_from_range(off_reader.get_point_cloud(), max_alpha_square); } /** \brief Alpha_complex constructor from a list of points. @@ -164,23 +158,7 @@ class Alpha_complex : public Simplex_tree<> { Alpha_complex(const InputPointRange& points, Filtration_value max_alpha_square = std::numeric_limits<Filtration_value>::infinity()) : triangulation_(nullptr) { - auto first = std::begin(points); - auto last = std::end(points); - - if (first != last) { - // point_dimension function initialization - Point_Dimension point_dimension = kernel_.point_dimension_d_object(); - - // Delaunay triangulation is point dimension. - triangulation_ = new Delaunay_triangulation(point_dimension(*first)); - - size_type inserted = triangulation_->insert(first, last); - if (inserted != (last -first)) { - std::cerr << "Alpha_complex - insertion failed " << inserted << " != " << (last -first) << "\n"; - exit(-1); // ----- >> - } - init(max_alpha_square); - } + init_from_range(points, max_alpha_square); } /** \brief Alpha_complex destructor. @@ -191,6 +169,12 @@ class Alpha_complex : public Simplex_tree<> { delete triangulation_; } + // Forbid copy/move constructor/assignment operator + Alpha_complex(const Alpha_complex& other) = delete; + Alpha_complex& operator= (const Alpha_complex& other) = delete; + Alpha_complex (Alpha_complex&& other) = delete; + Alpha_complex& operator= (Alpha_complex&& other) = delete; + /** \brief get_point returns the point corresponding to the vertex given as parameter. * * @param[in] vertex Vertex handle of the point to retrieve. @@ -202,6 +186,44 @@ class Alpha_complex : public Simplex_tree<> { } private: + template<typename InputPointRange > + void init_from_range(const InputPointRange& points, Filtration_value max_alpha_square) { + auto first = std::begin(points); + auto last = std::end(points); + if (first != last) { + // point_dimension function initialization + Point_Dimension point_dimension = kernel_.point_dimension_d_object(); + + // Delaunay triangulation is point dimension. + triangulation_ = new Delaunay_triangulation(point_dimension(*first)); + + std::vector<Point_d> points(first, last); + + // Creates a vector {0, 1, ..., N-1} + std::vector<std::ptrdiff_t> indices(boost::counting_iterator<std::ptrdiff_t>(0), + boost::counting_iterator<std::ptrdiff_t>(points.size())); + + // Sort indices considering CGAL spatial sort + typedef CGAL::Spatial_sort_traits_adapter_d<Kernel, Point_d*> Search_traits_d; + spatial_sort(indices.begin(),indices.end(),Search_traits_d(&(points[0]))); + + typename Delaunay_triangulation::Full_cell_handle hint; + for (auto index : indices) { + typename Delaunay_triangulation::Vertex_handle pos = triangulation_->insert(points[index], hint); + // Save index value as data to retrieve it after insertion + pos->data() = index; + hint = pos->full_cell(); + } + + if (triangulation_->number_of_vertices() != (last -first)) { + std::cerr << "Alpha_complex - insertion failed " << triangulation_->number_of_vertices() << " != " << + (last -first) << "\n"; + exit(-1); // ----- >> + } + init(max_alpha_square); + } + } + /** \brief Initialize the Alpha_complex from the Delaunay triangulation. * * @param[in] max_alpha_square maximum for alpha square value. @@ -233,18 +255,15 @@ class Alpha_complex : public Simplex_tree<> { // -------------------------------------------------------------------------------------------- // double map to retrieve simplex tree vertex handles from CGAL vertex iterator and vice versa - // Start to insert at handle = 0 - default integer value - Vertex_handle vertex_handle = Vertex_handle(); // Loop on triangulation vertices list for (CGAL_vertex_iterator vit = triangulation_->vertices_begin(); vit != triangulation_->vertices_end(); ++vit) { if (!triangulation_->is_infinite(*vit)) { #ifdef DEBUG_TRACES - std::cout << "Vertex insertion - " << vertex_handle << " -> " << vit->point() << std::endl; + std::cout << "Vertex insertion - " << vit->data() << " -> " << vit->point() << std::endl; #endif // DEBUG_TRACES - vertex_iterator_to_handle_.emplace(vit, vertex_handle); - vertex_handle_to_iterator_.push_back(vit); - vertex_handle++; + vertex_iterator_to_handle_.emplace(vit, vit->data()); + vertex_handle_to_iterator_.emplace(vit->data(), vit); } } // -------------------------------------------------------------------------------------------- diff --git a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp index 315582d1..80b39924 100644 --- a/src/Alpha_complex/test/Alpha_complex_unit_test.cpp +++ b/src/Alpha_complex/test/Alpha_complex_unit_test.cpp @@ -32,8 +32,6 @@ #include <string> #include <vector> -// to construct a Delaunay_triangulation from a OFF file -#include <gudhi/Delaunay_triangulation_off_io.h> #include <gudhi/Alpha_complex.h> // Use dynamic_dimension_tag for the user to be able to set dimension |