NAME

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plot_PD - Plot a persistence diagram as a color histogram or contour plot

SYNOPSIS

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homcloud-plot-PD
    [-h] [-V] -d DEGREE [-T TYPE] [-N] [-p POWER] [-l]
    [--loglog] [--linear-midpoint LINEAR_MIDPOINT] [-m MAX]
    [--vmin VMIN] [-c COLORMAP] [-s STYLE] [-t TITLE]
    [-U UNIT_NAME] [--font-size FONT_SIZE] [--aspect ASPECT]
    [--plot-essential] [-D SCATTERING_SIZE] [-o OUTPUT]
    [-x X_RANGE] [-X XBINS] [-y Y_RANGE] [-Y YBINS]
    [-n NORMALIZE_CONSTANT] [-M MARKER] [--dpi DPI]
    [--tight-layout]
    INPUT [INPUT ...]

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

ALIAS

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homcloud-plot-PD

DESCRIPTION

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This program plots a persistence diagram given by INPUT as a 2D histogram (color histogram by default, or a contour plot).

You can control the histogram binning with the -x/-X (birth axis) and -y/-Y (death axis) options. If they are not given, the range and number of bins are chosen automatically.

You can use multiple input files. In that case, all pairs from all files are merged into one diagram before plotting.

OPTIONS

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-h, --help            show this help message and exit
-V, --version         show program's version number and exit
-d DEGREE, --degree DEGREE
                      degree of PH
-T TYPE, --type TYPE  input file format (pdgm, text) (default:
                      autodetect)
-N, --negate          flip the sign of birth/death times for superlevel
                      persistence (default: False)
-p POWER, --power POWER
                      Output x^POWER for each value x
-l, --log             Output log(x+1) for each value x
--loglog              Output log(log(x+1)+1)
--linear-midpoint LINEAR_MIDPOINT
                      linear with midpoint
-m MAX, --vmax MAX    Maximum of colorbar (default: autoscale)
--vmin VMIN           Minimum of colorbar
-c COLORMAP, --colormap COLORMAP
                      matplotlib colormap name
-s STYLE, --style STYLE
                      plotting style (colorhistogram(default), contour)
-t TITLE, --title TITLE
                      title string
-U UNIT_NAME, --unit-name UNIT_NAME
                      The unit name of birth and death times
--font-size FONT_SIZE
                      font size (default: 12)
--aspect ASPECT       histogram aspect (default: auto)
--plot-essential      whether to plot essential values (default: False)
-D SCATTERING_SIZE, --diffuse-pairs SCATTERING_SIZE
                      Diffuse pairs using gaussian distribution of SD=SIGMA
-o OUTPUT, --output OUTPUT
                      output file
-x X_RANGE, --x-range X_RANGE
                      birth range
-X XBINS, --xbins XBINS
                      number of bins in birth-axis
-y Y_RANGE, --y-range Y_RANGE
                      death range
-Y YBINS, --ybins YBINS
                      number of bins in death-axis
-n NORMALIZE_CONSTANT, --normalize-constant NORMALIZE_CONSTANT
                      normalize constant to histogram height
-M MARKER, --marker MARKER
                      marker file
--dpi DPI             output DPI (used with -o option, default is
                      savefig.dpi for matplotlib)
--tight-layout        use tight layout (adjusting layout)

INPUT FORMAT

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A .pdgm file, or a text file of birth-death pairs (one pair per line, -d is ignored in that case):

birth1 death1
birth2 death2
   :

-T selects the format explicitly; by default it is auto-detected from the file content/extension.

OUTPUT FORMAT

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If the output argument is not given, the plotted picture is shown in your display. If the output argument is given, the output format is determined by its extension. You can output the picture in PNG (.png), PDF (.pdf), and EPS (.eps). Other formats are also available if matplotlib supports them.