NAME
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pict.pixel_levelset_nd - Compute a persistence diagram from an N-dimensional picture by using a cubical sublevel/superlevel filtration

SYNOPSIS
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homcloud-pict-pixel-levelset-nd
    [-h] [-V] [-m MODE] [-T TYPE] [-C] -o OUTPUT
    [-p PERIODIC] [--algorithm ALGORITHM]
    [-M SAVE_BOUNDARY_MAP] [--license]
    [input ...]

This program can also be invoked as python3 -m homcloud.cli.pict.pixel_levelset_nd.

ALIAS
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homcloud-pict-pixel-levelset-nd

DESCRIPTION
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This program computes a persistence diagram from a cubical sublevel-set (or superlevel-set) filtration constructed from the given N-dimensional picture data, and writes it as a .pdgm file.

-m sublevel (the default) filters cells in increasing order of pixel value; -m superlevel filters in decreasing order.

-C/--cubical switches from the (fast, default) bitmap-based cubical filtration to an explicit cubical complex filtration, which is slower but is required by some downstream tools.

OPTIONS
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-h, --help            show this help message and exit
-V, --version         show program's version number and exit
-m MODE, --mode MODE  filtraty type (sublevel(default),superlevel)
-T TYPE, --type TYPE  input data format
                      (text2d,text_nd(default),picture2d,pictures3d,npy)
-C, --cubical         Use explicit cubical filtration (slow)
-o OUTPUT, --output OUTPUT
                      output file
-p PERIODIC, --periodic PERIODIC
                      periodic (example: 0,1,1 for y and z are periodic)
--algorithm ALGORITHM
                      algorithm (dipha, phat-twist, phat-chunk-parallel)
-M SAVE_BOUNDARY_MAP, --save-boundary-map SAVE_BOUNDARY_MAP
                      save boundary map (yes/no, default:no)
--license             show license and exit

-M/--save-boundary-map requires -C/--cubical; giving -M on without -C is an error. Saving the boundary map is what makes the output usable later with homcloud-optvol.

INPUT FILE FORMAT
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The program accepts the following types of file formats: text2d, text_nd, picture2d, pictures3d and npy.

text2d
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2D pixel (floating point number) values represented by a text as follows:

x_11 x_12 ... x_1n
x_21 x_22 ... x_2n
 :    :        :
x_m1 x_m2 ... x_mn

Each coefficient should be floating point numbers.

text_nd
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N-dimensional pixel (floating point number) values represented by a text as in the following format:

First line represents the shape of data. For example, if the shape of your data is 200x230x250, first line should be 200 230 250.
The following lines are floating point number values in x-fastest direction
A line starting with # is skipped as a comment
An empty line is also skipped.

An example is as follows:

# 4x3x2 3D voxel data
4 3 2

1 2 3 4
5 6 7 8
9 10 11 12

13 14 15 16
17 18 19 20
21 22 23 24

picture2d
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A gray scale PNG or TIFF file.

If the input file is 16bit grayscale file, the pixel value is normalized to the range of 0 .. 255.

pictures3d
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Gray scale PNG or TIFF files. All picture sizes must be same. If not, an error occurs. All pictures are stacked in the commandline order.

If the input file is 16bit grayscale file, the pixel value is normalized to the range of 0 .. 255.

npy
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Numpy’s npy file.

Please see https://docs.scipy.org/doc/numpy/neps/npy-format.html for details of this format.

OUTPUT FORMAT
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The program always writes a .pdgm file into OUTPUT. Old output formats (.complex, .icomplex, .diagram, .idiagram) are no longer supported; giving OUTPUT one of these extensions raises an error.

NOTES
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The old -I/--combine-index-map and -D/--convert-to-diagram options (used when the program produced dipha/idipha complex or diagram files) have been removed: the program always computes and writes a pdgm file directly now. The old -u/--upper-bound and -l/--lower-bound options documented previously do not exist in the current implementation.

NAME#

SYNOPSIS#

ALIAS#

DESCRIPTION#

OPTIONS#

INPUT FILE FORMAT#

text2d#

text_nd#

picture2d#

pictures3d#

npy#

OUTPUT FORMAT#

NOTES#