`PyLogik`

A Python package dedicated to sharing functions and classes for common image processing and statistical tools. This includes Sorensen–Dice coefficient (Dice) score and plotting functions.

Citing this work:

A. Kline, PyLogik, 2022

Integration with Jupyter Lab/Jupyter Notebooks
Built-in plotting functionality for image comparisons

Installation
Package Import
Data Import
Dice Score Calculation
Impairshow
Conclusion

Installation

Install the package through pip:

$ pip install pylogik

Image Processing Import

from pylogik.image import im_analysis

Data Import

Options for reading in images:

Matplotlib - plt.imread()
OpenCV - cv2.imread()
Pillow - Image.open()
scikit-image - io.imread()

# read in your data
im1 = cv2.imread('example_im1.png')
im2 = cv2.imread('example_im2.png')

Dice Score

The mathematical formalism of the Dice score is denoted by the equation:

$$ DSC = \frac{2*|X \cap Y|}{|X|+ |Y|} $$

where $\cap$ denotes the intersection of two images $X$ and $Y$.

Performing the calculation using a function in PyLogik:

dice = im_analysis.dice_score(pred, true, k=1)

Note:

pred - array of the predicted segmentation
true - array of the ground truth segmentation
k - value to perform matching on (default = 1)
Returns: dice score (float)

Impairshow Graphical Output

imshowpair returns the array and image associated with a dice score comparison of 2 logical images. Colors are prespecified as magenta and green but can be adjusted by the user.

im_analysis.imshowpair(pred, true, color1 = (124,252,0), color2 = (255,0,252), show_fig = True):

Note:

pred - array of the predicted segmentation
true - array of the ground truth segmentation
color1 - first color to show unique values from first image
color2 - second color to show unique values from second image
Returns: array and graphical plot

Conclusion

This package offers a user friendly dice score calculation and dice score plotting functionality to showcase the intersection and complement of each image relative to the other. This package will be continually built on to incorporate other statistical and image processing functionality

adriennekline/pylogik

PyLogik