From c0947c634c1babc37699d896a961d80979db1327 Mon Sep 17 00:00:00 2001 From: Ulrich Bauer Date: Sat, 23 Jul 2016 13:30:13 +0200 Subject: Typos and line endings in readme progress every 1000 reduced columns --- README.md | 184 +++++++++++++++++++++++++++++++------------------------------- 1 file changed, 92 insertions(+), 92 deletions(-) (limited to 'README.md') diff --git a/README.md b/README.md index 77eec68..4b4600e 100644 --- a/README.md +++ b/README.md @@ -1,72 +1,72 @@ -# Ripser - -Copyright © 2015–2016 [Ulrich Bauer]. - - -### Description - -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. - -The main features of Ripser: - - - time- and memory-efficient - - support for coefficients in prime finite fields - - less than 1000 lines of code in a single C++ file - - no external dependencies (optional support for Google's [sparsehash]) - -Currently, Ripser outperforms other codes ([Dionysus], [DIPHA], [GUDHI], [Perseus], [PHAT]) by a factor of at least 40 in computation time and a factor of at least 15 in memory efficiency. (Note that [PHAT] does not contain code for generating Vietoris–Rips filtrations). - -Input formats currently supported by Ripser: - - - comma-separated lower triangular distance matrix (preferred) - - comma-separated lower triangular distance matrix (MATLAB output from the function `pdist`) - - [DIPHA] distance matrix data - -Ripser's efficiency is based on a few important concepts and principles: - - - Compute persistent *co*homology - - Don't compute information that is never needed - (for the experts: employ the *clearing* optimization, aka *persistence with a twist*) - - Don't store information that can be readily recomputed - - Take obvious shortcuts (*apparent persistence pairs*) - - -### Version -[Latest release][latest-release]: 1.0 (July 2016) - - -### Building - -Ripser requires a C++11 compiler. Here is how to obtain, build, and run Ripser: - -```sh -git clone https://github.com/Ripser/ripser.git -cd ripser -make -./ripser examples/sphere_3_192.lower_distance_matrix -``` - - -### Options - -Ripser supports several compile-time options. They are switched on by defining the C preprocessor macros listed below, either using `#define` in the code or by passing an argument to the compiler. The following options are supported: - - - `ASSEMBLE_REDUCTION_MATRIX`: store the reduction matrix; may speed up computation but will also increase memory usage - - `USE_COEFFICIENTS`: enable support for coeffitients in a prime field - - `INDICATE_PROGRESS`: indicate the current progress in the console - - `PRINT_PERSISTENCE_PAIRS`: output the computed persistence pairs (enabled by default) - - `USE_GOOGLE_HASHMAP`: enable support for Google's [sparsehash] data structure; may further reducue memory footprint - -Furthermore, one of the following options needs to be chosen to specify the format for the input files: - - - `FILE_FORMAT_LOWER_TRIANGULAR_CSV`: lower triangular distance matrix; a comma separated list of the distance matrix entries below the diagonal, sorted lexicographically by row index and column index - - `FILE_FORMAT_UPPER_TRIANGULAR_CSV`: upper triangular distance matrix; similar to the previous, but for the entries above the diagonal; suitable for output from the MATLAB function `pdist`, saved in a CSV file - - `FILE_FORMAT_DIPHA`: DIPHA distance matrix as described on the [DIPHA] website - -For example, to build with support for coefficients: - -```sh -$ c++ -std=c++11 ripser.cpp -o ripser -Ofast -D NDEBUG -D FILE_FORMAT_LOWER_TRIANGULAR_CSV -D USE_COEFFICIENTS +# Ripser + +Copyright © 2015–2016 [Ulrich Bauer]. + + +### Description + +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. + +The main features of Ripser: + + - time- and memory-efficient + - support for coefficients in prime finite fields + - less than 1000 lines of code in a single C++ file + - 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). + +Input formats currently supported by Ripser: + + - comma-separated lower triangular distance matrix (preferred) + - comma-separated lower triangular distance matrix (MATLAB output from the function `pdist`) + - [DIPHA] distance matrix data + +Ripser's efficiency is based on a few important concepts and principles: + + - Compute persistent *co*homology + - Don't compute information that is never needed + (for the experts: employ the *clearing* optimization, aka *persistence with a twist*) + - Don't store information that can be readily recomputed + - Take obvious shortcuts (*apparent persistence pairs*) + + +### Version +[Latest release][latest-release]: 1.0 (July 2016) + + +### Building + +Ripser requires a C++11 compiler. Here is how to obtain, build, and run Ripser: + +```sh +git clone https://github.com/Ripser/ripser.git +cd ripser +make +./ripser examples/sphere_3_192.lower_distance_matrix +``` + + +### Options + +Ripser supports several compile-time options. They are switched on by defining the C preprocessor macros listed below, either using `#define` in the code or by passing an argument to the compiler. The following options are supported: + + - `ASSEMBLE_REDUCTION_MATRIX`: store the reduction matrix; may speed up computation but will also increase memory usage + - `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) + - `USE_GOOGLE_HASHMAP`: enable support for Google's [sparsehash] data structure; may further reducue memory footprint + +Furthermore, one of the following options needs to be chosen to specify the format for the input files: + + - `FILE_FORMAT_LOWER_TRIANGULAR_CSV`: lower triangular distance matrix; a comma separated list of the distance matrix entries below the diagonal, sorted lexicographically by row index and column index + - `FILE_FORMAT_UPPER_TRIANGULAR_CSV`: upper triangular distance matrix; similar to the previous, but for the entries above the diagonal; suitable for output from the MATLAB function `pdist`, saved in a CSV file + - `FILE_FORMAT_DIPHA`: DIPHA distance matrix as described on the [DIPHA] website + +For example, to build with support for coefficients: + +```sh +$ c++ -std=c++11 ripser.cpp -o ripser -Ofast -D NDEBUG -D FILE_FORMAT_LOWER_TRIANGULAR_CSV -D USE_COEFFICIENTS ``` The following options are supported at the command line: @@ -75,27 +75,27 @@ The following options are supported at the command line: - `--threshold t`: compute Rips complexes up to diameter *t* - `--modulus p`: compute homology with coefficients in the prime field Z/*p*Z (only available when build with the option `USE_COEFFICIENTS`) - -### Planned features - -The following features are currently planned for future versions: - - - support for point clouds - - computation of representative cycles for persistent homology (currenly only *co*cycles are computed) - - support for sparse distance matrices - - -### License - -[LGPL] 3.0 - - -[Ulrich Bauer]: -[latest-release]: -[Dionysus]: -[DIPHA]: -[PHAT]: -[Perseus]: -[GUDHI]: -[sparsehash]: + +### Planned features + +The following features are currently planned for future versions: + + - support for point clouds + - computation of representative cycles for persistent homology (currenly only *co*cycles are computed) + - support for sparse distance matrices + + +### License + +[LGPL] 3.0 + + +[Ulrich Bauer]: +[latest-release]: +[Dionysus]: +[DIPHA]: +[PHAT]: +[Perseus]: +[GUDHI]: +[sparsehash]: [LGPL]: \ No newline at end of file -- cgit v1.2.3