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Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 14 |
1 files changed, 10 insertions, 4 deletions
@@ -7,6 +7,8 @@ Copyright © 2015–2016 [Ulrich Bauer]. Ripser is a lean C++ code for the computation of Vietoris–Rips persistence barcodes. It can do just this one thing, but does it extremely well. +To see a live demo of Ripser's capabilities, go to [live.ripser.org]. The computation happens inside the browser (using [PNaCl] on Chrome and JavaScript via [Emscripten] on other browsers). + The main features of Ripser: - time- and memory-efficient @@ -14,7 +16,7 @@ The main features of Ripser: - support for coefficients in prime finite fields - no external dependencies (optional support for Google's [sparsehash]) -Currently, Ripser outperforms other codes ([Dionysus], [DIPHA], [GUDHI], [Perseus], [PHAT]) by a factor of more than 40 in computation time and a factor of more than 15 in memory efficiency. (Note that [PHAT] does not contain code for generating Vietoris–Rips filtrations). +Currently, Ripser outperforms other codes ([Dionysus], [DIPHA], [GUDHI], [Perseus], [PHAT]) by a factor of more than 40 in computation time and a factor of more than 15 in memory efficiency (for the example linked at [live.ripser.org]). (Note that [PHAT] does not contain code for generating Vietoris–Rips filtrations). Input formats currently supported by Ripser: @@ -57,7 +59,7 @@ Ripser supports several compile-time options. They are switched on by defining t - `USE_COEFFICIENTS`: enable support for coefficients in a prime field - `INDICATE_PROGRESS`: indicate the current progress in the console - `PRINT_PERSISTENCE_PAIRS`: output the computed persistence pairs (enabled by default in the code; comment out to disable) - - `USE_GOOGLE_HASHMAP`: enable support for Google's [sparsehash] data structure; may further reducue memory footprint + - `USE_GOOGLE_HASHMAP`: enable support for Google's [sparsehash] data structure; may further reduce memory footprint For example, to build Ripser with support for coefficients: @@ -72,7 +74,7 @@ The input is given either in a file whose name is passed as an argument, or thro - `--format`: use the specified file format for the input. The following formats are supported: - `lower-distance` (default if no format is specified): lower triangular distance matrix; a comma (or whitespace, or other non-numerical character) separated list of the distance matrix entries below the diagonal, sorted lexicographically by row index, then column index - `upper-distance`: upper triangular distance matrix; similar to the previous, but for the entries above the diagonal; suitable for output from the MATLAB functions `pdist` or `seqpdist`, exported to a CSV file - - `distances`: full distance matrix; similar to the above, but for all entries of the distance matrix + - `distance`: full distance matrix; similar to the above, but for all entries of the distance matrix - `dipha`: DIPHA distance matrix as described on the [DIPHA] website - `point-cloud`: point cloud; a comma (or whitespace, or other non-numerical character) separated list of coordinates of the points in some Euclidean space, one point per line - `--dim k`: compute persistent homology up to dimension *k* @@ -89,13 +91,17 @@ The following features are currently planned for future versions: - computation of representative cycles for persistent homology (currenly only *co*cycles are computed) - support for sparse distance matrices +Prototype implementations are already avaliable; please contact the author if one of these features might be relevant for your research. + ### License Ripser is licensed under the [LGPL] 3.0. Please contact the author if you want to use Ripser in your software under a different license. - [Ulrich Bauer]: <http://ulrich-bauer.org> +[live.ripser.org]: <http://live.ripser.org> +[PNaCl]: <https://www.chromium.org/nativeclient/pnacl/> +[Emscripten]: <http://emscripten.org> [latest-release]: <https://github.com/Ripser/ripser/releases/latest> [Dionysus]: <http://www.mrzv.org/software/dionysus/> [DIPHA]: <http://git.io/dipha> |