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updated readme

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ubauer committed May 22, 2019
1 parent 4879faf commit 2623d262762fed4c8db15b034f5881fc9fa9813d
Showing with 9 additions and 9 deletions.
  1. +9 −9 README.md
@@ -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`).

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