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ImageCleanup.py
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ImageCleanup.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Jun 11 23:16:19 2020
@author: Wayan A. Fontaine-Seiler
EXTENSION
Image Cleanup Extension for use in the main registration program
Dependencies: None
"""
## ROUGHT IMAGE CLEANUP PROGRAM (AFTER TRANSFORM BY SIMPLEELASTIX)##
import numpy as np
import matplotlib as plt
from PIL import Image # Image manipulation in Python
def IsArtefact(image_nda_unint8,i,j,aggres):
sum_pix=0
sum_pix=sum_pix+image_nda_unint8[i,j+1]
sum_pix=sum_pix+image_nda_unint8[i,j-1]
sum_pix=sum_pix+image_nda_unint8[i+1,j]
sum_pix=sum_pix+image_nda_unint8[i-1,j]
sum_pix=sum_pix+image_nda_unint8[i-1,j-1]
sum_pix=sum_pix+image_nda_unint8[i-1,j+1]
sum_pix=sum_pix+image_nda_unint8[i+1,j+1]
sum_pix=sum_pix+image_nda_unint8[i+1,j-1]
avg_pix=sum_pix/8
if avg_pix<aggres:
return True
else:
return False
def AveragePix(image_nda_unint8,i,j):
sum_pix=0
sum_pix=sum_pix+image_nda_unint8[i,j+1]
sum_pix=sum_pix+image_nda_unint8[i,j-1]
sum_pix=sum_pix+image_nda_unint8[i+1,j]
sum_pix=sum_pix+image_nda_unint8[i-1,j]
sum_pix=sum_pix+image_nda_unint8[i-1,j-1]
sum_pix=sum_pix+image_nda_unint8[i-1,j+1]
sum_pix=sum_pix+image_nda_unint8[i+1,j+1]
sum_pix=sum_pix+image_nda_unint8[i+1,j-1]
avg_pix=sum_pix/8
return avg_pix
def ImageCleanup(img_nda_unint8,thres,aggres):
img_nda=img_nda_unint8
for i in range(1,len(img_nda[0])-1):
for j in range(1,len(img_nda)-1):
if img_nda[i][j]>=thres:
if IsArtefact(img_nda, i, j,aggres)==True:
img_nda[i][j]=AveragePix(img_nda, i, j)
return img_nda