Element_PI.VariancePersist

Element_PI.VariancePersist(pixelx=100, pixely=100, myspread=2, myspecs={'maxBD': 2, 'minBD': 0}, showplot=True)

Generate a persistence image given a file with coordinates of atoms.

Includes difference in electronegativity.

Parameters

• Filename (string) –

  • Name of file with chemical data to read

• pixelx (int, optional) –

  • Default value = 100

  • Number of pixels on x-axis

• pixely (int, optional) –

  • Default value = 100

  • Number of pixels on y-axis

• myspread (int, optional) –

  • Default value = 2

  • Parameter for kernel

  • For Gaussian kernel, this specifies the variance

• myspecs (dictionary, optional) –

  • Default value = {"maxBD": 2, "minBD":0}

  • Specifies boundary extent in Angstroms

  • Format:

    {
        "maxBD": <float>,
        "minBD": <float>
    }
    

  • maxBD: upper boundary of persistence image (in Angstroms)

  • minBD: lower boundary of persistence image (in Angstroms)

• showplot (bool, optional) –

  • Default value = True

  • Options:

    • True: plot the PI once generated

    • False: do not plot the PI

Returns

img_array –

• One-dimensional vector representation of a persistence image

Return type

Numpy array

Example

The following example demonstrates how to create a persistence image based on chemical data found in the compound.xyz file:

from Element_PI import VariancePersist

# Size of generated image is 10x10
pix_y  = 10
pix_x  = 10

spread = 2 # Set variance to 2
specs  = {'maxBD': 2, 'minBD': 0}

PI_vector = VariancePersist('compound.xyz',
                            pixelx = pix_x,
                            pixely = pix_y,
                            myspread = spread
                            myspecs = specs,
                            showplot = True)

An example of the image output by running the above code would be: