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| build: | ||
| build: ripser | ||
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| all: ripser ripser_coeff ripser_dipha ripser_dipha_coeff | ||
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| ripser: ripser.cpp | ||
| c++ -std=c++11 ripser.cpp -o ripser -Ofast -D NDEBUG -D FILE_FORMAT_LOWER_TRIANGULAR_CSV | ||
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| coefficients: | ||
| ripser_coeff: ripser.cpp | ||
| c++ -std=c++11 ripser.cpp -o ripser_coeff -Ofast -D NDEBUG -D FILE_FORMAT_LOWER_TRIANGULAR_CSV -D USE_COEFFICIENTS | ||
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| ripser_dipha: ripser.cpp | ||
| c++ -std=c++11 ripser.cpp -o ripser_dipha -Ofast -D NDEBUG -D FILE_FORMAT_DIPHA | ||
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| ripser_dipha_coeff: ripser.cpp | ||
| c++ -std=c++11 ripser.cpp -o ripser_dipha_coeff -Ofast -D NDEBUG -D FILE_FORMAT_DIPHA -D USE_COEFFICIENTS | ||
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| clean: | ||
| rm ripser ripser_coeff ripser_dipha ripser_dipha_coeff |
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| # Ripser | ||
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| Copyright © 2015–2016 [Ulrich Bauer]. | ||
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| ### Description | ||
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| 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. | ||
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| The main features of Ripser: | ||
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| - 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]) | ||
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| 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). | ||
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| Input formats currently supported by Ripser: | ||
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| - comma-separated lower triangular distance matrix (preferred) | ||
| - comma-separated lower triangular distance matrix (MATLAB output from the function `pdist`) | ||
| - [DIPHA] distance matrix data | ||
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| Ripser's efficiency is based on a few important concepts and principles: | ||
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| - 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*) | ||
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| ### Version | ||
| [Latest release][latest-release]: 1.0 (July 2016) | ||
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| ### Building | ||
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| Ripser requires a C++11 compiler. Here is how to obtain, build, and run Ripser: | ||
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| ```sh | ||
| git clone https://github.com/Ripser/ripser.git | ||
| cd ripser | ||
| make | ||
| ./ripser examples/sphere_3_192.lower_distance_matrix | ||
| ``` | ||
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| ### Options | ||
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| 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: | ||
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| - `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 | ||
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| Furthermore, one of the following options needs to be chosen to specify the format for the input files: | ||
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| - `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 | ||
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| For example, to build with support for coefficients: | ||
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| ```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 | ||
| - less than 1000 lines of code in a single C++ file | ||
| - 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). | ||
|
|
||
| Input formats currently supported by Ripser: | ||
|
|
||
| - comma-separated values lower triangular distance matrix (preferred) | ||
| - comma-separated values upper 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 (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 | ||
| - `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 | ||
|
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||
| 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 | ||
| ``` | ||
|
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| The following options are supported at the command line: | ||
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| - `--top_dim k`: compute persistent homology up to dimension *k* | ||
| - `--dim k`: compute persistent homology up to dimension *k* | ||
| - `--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`) | ||
|
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| ### Planned features | ||
|
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| The following features are currently planned for future versions: | ||
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| - support for point clouds | ||
| - computation of representative cycles for persistent homology (currenly only *co*cycles are computed) | ||
| - support for sparse distance matrices | ||
|
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| ### License | ||
|
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| [LGPL] 3.0 | ||
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||
|
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| [Ulrich Bauer]: <http://ulrich-bauer.org> | ||
| [latest-release]: <https://github.com/Ripser/ripser/releases/latest> | ||
| [Dionysus]: <http://www.mrzv.org/software/dionysus/> | ||
| [DIPHA]: <http://git.io/dipha> | ||
| [PHAT]: <http://git.io/dipha> | ||
| [Perseus]: <http://www.sas.upenn.edu/~vnanda/perseus/> | ||
| [GUDHI]: <http://gudhi.gforge.inria.fr> | ||
| [sparsehash]: <https://github.com/sparsehash/sparsehash> | ||
|
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| ### 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 | ||
|
|
||
|
|
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| ### License | ||
|
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||
| [LGPL] 3.0 | ||
|
|
||
|
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| [Ulrich Bauer]: <http://ulrich-bauer.org> | ||
| [latest-release]: <https://github.com/Ripser/ripser/releases/latest> | ||
| [Dionysus]: <http://www.mrzv.org/software/dionysus/> | ||
| [DIPHA]: <http://git.io/dipha> | ||
| [PHAT]: <http://git.io/dipha> | ||
| [Perseus]: <http://www.sas.upenn.edu/~vnanda/perseus/> | ||
| [GUDHI]: <http://gudhi.gforge.inria.fr> | ||
| [sparsehash]: <https://github.com/sparsehash/sparsehash> | ||
| [LGPL]: <https://www.gnu.org/licenses/lgpl> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,13 +1,13 @@ | ||
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| 1, | ||
| 1,2, | ||
| 1,2,2, | ||
| 1,2,2,2, | ||
| 1,1,2,1,2, | ||
| 1,2,1,2,1,2, | ||
| 1,1,2,2,1,2,2, | ||
| 1,2,1,1,2,2,2,2, | ||
| 2,1,1,2,2,1,1,1,1, | ||
| 2,2,2,2,2,1,1,2,2,1, | ||
| 2,2,2,2,2,2,2,1,1,1,2, | ||
| 2,2,2,1,1,1,1,1,1,2,1,1, | ||
| 1 | ||
| 1,2 | ||
| 1,2,2 | ||
| 1,2,2,2 | ||
| 1,1,2,1,2 | ||
| 1,2,1,2,1,2 | ||
| 1,1,2,2,1,2,2 | ||
| 1,2,1,1,2,2,2,2 | ||
| 2,1,1,2,2,1,1,1,1 | ||
| 2,2,2,2,2,1,1,2,2,1 | ||
| 2,2,2,2,2,2,2,1,1,1,2 | ||
| 2,2,2,1,1,1,1,1,1,2,1,1 |
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