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author | Ulrich Bauer <mail@ulrich-bauer.org> | 2019-05-22 20:13:17 +0200 |
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committer | Ulrich Bauer <mail@ulrich-bauer.org> | 2019-05-22 20:13:17 +0200 |
commit | 2623d262762fed4c8db15b034f5881fc9fa9813d (patch) | |
tree | f54da91ad54ec64cf7d7352b89832a28590a08f5 /README.md | |
parent | 4879faf147e96923952b248ed2552c10eb1e809c (diff) |
updated readme
Diffstat (limited to 'README.md')
-rw-r--r-- | README.md | 18 |
1 files changed, 9 insertions, 9 deletions
@@ -20,7 +20,7 @@ Currently, Ripser outperforms other codes ([Dionysus], [DIPHA], [GUDHI], [Perseu Input formats currently supported by Ripser: - - comma-separated values lower triangular distance matrix (preferred) + - comma-separated values lower triangular distance matrix - comma-separated values upper triangular distance matrix (MATLAB output from the function `pdist`) - comma-separated values full distance matrix - [DIPHA] distance matrix data @@ -73,14 +73,14 @@ A Makefile is provided with some variants of the above options. Use `make all` t The input is given either in a file whose name is passed as an argument, or through stdin. The following options are supported at the command line: - `--format`: use the specified file format for the input. The following formats are supported: - - `lower-distance` (default if no format is specified): 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 - - `upper-distance`: upper triangular distance matrix; similar to the previous, but for the entries above the diagonal; suitable for output from the MATLAB functions `pdist` or `seqpdist`, exported to a CSV file - - `distance`: full distance matrix; similar to the above, but for all entries of the distance matrix - - `dipha`: DIPHA distance matrix as described on the [DIPHA] website - - `point-cloud`: point cloud; a comma (or whitespace, or other non-numerical character) separated list of coordinates of the points in some Euclidean space, one point per line - - `--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 built with the option `USE_COEFFICIENTS`) + - `lower-distance` (default if no format is specified): 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. + - `upper-distance`: upper triangular distance matrix; similar to the previous, but for the entries above the diagonal; suitable for output from the MATLAB functions `pdist` or `seqpdist`, exported to a CSV file. + - `distance`: full distance matrix; similar to the above, but for all entries of the distance matrix. One line per row of the matrix; only the part below the diagonal is actually read. + - `dipha`: DIPHA distance matrix as described on the [DIPHA] website. + - `point-cloud`: point cloud; a comma (or whitespace, or other non-numerical character) separated list of coordinates of the points in some Euclidean space, one point per line. + - `--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 built with the option `USE_COEFFICIENTS`). |