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Diffstat (limited to 'README.md')
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1 files changed, 4 insertions, 4 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 |