NAME

pc_alpha - Compute a persistence diagram from alpha filtration

SYNOPSIS

python3 -m homcloud.pc2diphacomplex
        [-h] [-t TYPE] [-n NOISE] 
        [-d DIMENSION] [-w] [--no-square] [-I] [-P] [-A]
        INPUT OUTPUT

ALIAS

homcloud-pc-alpha

DESCRIPTION

This program computes (weighted and non-weighted) alpha filtration for dipha from (weighted or non-weighted) point clouds.

OPTIONS

-h, --help            show this help message and exit
-V, --version         show program's version number and exit
-t TYPE, --type TYPE  Input file format type
-n NOISE, --noise NOISE
                      level of additive noise
-d DIMENSION, --dimension DIMENSION
                      dimension of the input data
-w, --weighted        use an weighed alpha filtraion
--no-square           no squared output, if a birth radius is negative, the
                      output is -sqrt(abs(r))
-I, --combine-index-map
                      combine the index map with the output filtration
-D, --convert-to-diagram
                      call dipha and directly convert to a diagram
-P, --partial-filtration
                      Compute partial filtration (relative homology)
-A, --check-acyclicity
                      Check acyclicity for paritial filtration
-M SAVE_BOUNDARY_MAP, --save-boundary-map SAVE_BOUNDARY_MAP
                      save boundary map into idiagram file(only available
                      with phat-* algorithms, *on*/off)
--algorithm ALGORITHM
                      algorithm (dipha, phat-twist(default), phat-chunk-
                      parallel)
--vertex-symbols VERTEX_SYMBOLS
                      vertex symbols file
--license             show license and exit

INPUT FILE FORMAT

You can use both weighed alpha filtraiton and non-weighted alpha filtration.

The input format of a non-weighted 3d point cloud of is:

# A line starting with sharp sign is ignored
x_1 y_1 z_1
x_2 y_2 z_2
:

You can use 2d point cloud:

x_1 y_1
x_2 y_2
  :

In the weighted case, the input file for 3d is:

x_1 y_1 z_1 w_1
x_2 y_2 z_2 w_2
   :

The weights should be squared (for example, you should put the square of vanderwaals radius. The lines starting with sharp sign are always ignored.

Now 2d weighted alpha filtration is not supported because of the limitation of cgal.

OUTPUT FILE

If -D option is given, the output file is a diagram data. In this case, a persistence diagram is computed from the boundary matrix. dipha's diagram file is written if -I option is not given, and indexed-diagram file (idiagarm) file is written if -I option is given.

NOTES

This module was previously named pc2diphacomplex and renamed to pc_alpha. Now the name pc2diphacomplex is obsolete.

Now the usage of -D option is always reocommend. This option is planned to be mandatory and removed in a future version.