Image cleaner module

This module takes clear of cleaning up the junk from outside the brain area by using masks.

class library.image_manipulation.image_cleaner.ImageCleaner

Bases: object

Methods for cleaning images [and rotation, if necessary]. ‘Cleaning’ means applying user-verified masks (QC step) to downsampled or full-resolution images

create_cleaned_images()

This method applies the image masks that has been edited by the user to extract the tissue image from the surrounding debris 1. Set up the mask, input and output directories 2. clean images 3. Get biggest box size from all contours from all files and update DB with that info 4. Place images in image size with correct background color

create_rotated_aligned_masks()

create_shell()

create_shell_from_mask()

mask_aligned_imageNOTUSED(img, file)

parallel_create_cleaned(INPUT, CLEANED, MASKS)

Do the image cleaning in parallel

Parameters:

• INPUT – str of file location input

• CLEANED – str of file location output

• MASKS – str of file location of masks

set_max_width_and_height()