diff options
| author | Ulrich Bauer <ulrich.bauer@tum.de> | 2016-07-25 01:00:04 +0200 |
|---|---|---|
| committer | Ulrich Bauer <ulrich.bauer@tum.de> | 2016-07-25 01:00:04 +0200 |
| commit | c383c3ee45b4ef1002e643da0bb29ed846367117 (patch) | |
| tree | 216580dd368b1f02d916f30874e8f1fb5e9ab421 | |
| parent | 7eaac02f7f7114da87583136ebc44f7086536337 (diff) | |
some cleanup
| -rw-r--r-- | README.md | 8 | ||||
| -rw-r--r-- | benchmarks/benchmarks.txt | 2 | ||||
| -rw-r--r-- | ripser.xcodeproj/project.pbxproj | 3 |
3 files changed, 5 insertions, 8 deletions
@@ -10,16 +10,16 @@ Ripser is a lean C++ code for the computation of Vietoris–Rips persistence bar 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 + - 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 lower triangular distance matrix (preferred) - - comma-separated lower triangular distance matrix (MATLAB output from the function `pdist`) + - 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: @@ -59,7 +59,7 @@ Ripser supports several compile-time options. They are switched on by defining t 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_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 diff --git a/benchmarks/benchmarks.txt b/benchmarks/benchmarks.txt index 679c5e7..c5fc91f 100644 --- a/benchmarks/benchmarks.txt +++ b/benchmarks/benchmarks.txt @@ -2,7 +2,7 @@ /usr/bin/time -l ~/Bitbucket/phat/benchmark --primal --bit_tree_pivot_column --twist ~/Bitbucket/phat-paper/benchmark/phat/sphere_3_192_coboundary.phat -/usr/bin/time -l ~/Bitbucket/dipha/dipha --benchmark --upper_dim 3 --dual ~/Bitbucket/phat-paper/benchmark/dipha/sphere_3_192.complex /dev/null +/usr/bin/time -l ~/Source/dipha/dipha --benchmark --upper_dim 3 --dual ~/Bitbucket/phat-paper/benchmark/dipha/sphere_3_192.complex /dev/null /usr/bin/time -l ~/Source/Gudhi_library_1.3.0/example/Persistent_cohomology/rips_persistence -d3 -p2 ~/Bitbucket/phat-paper/benchmark/point\ cloud/sphere_3_192_points.dat -o/dev/null diff --git a/ripser.xcodeproj/project.pbxproj b/ripser.xcodeproj/project.pbxproj index d924596..08adcbd 100644 --- a/ripser.xcodeproj/project.pbxproj +++ b/ripser.xcodeproj/project.pbxproj @@ -210,9 +210,6 @@ GCC_PREPROCESSOR_DEFINITIONS = ( "$(inherited)", FILE_FORMAT_UPPER_TRIANGULAR_CSV, - USE_COEFFICIENTS, - STORE_DIAMETERS, - PRINT_PERSISTENCE_PAIRS, ); PRODUCT_NAME = "$(TARGET_NAME)"; }; |