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authorUlrich Bauer <ulrich.bauer@tum.de>2016-07-23 13:30:13 +0200
committerUlrich Bauer <ulrich.bauer@tum.de>2016-07-23 13:30:13 +0200
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@@ -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]: <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>
+
+### 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]: <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> \ No newline at end of file