Automatically cropping an image with python/PIL

Issue

Can anyone help me figure out what’s happening in my image auto-cropping script? I have a png image with a large transparent area/space. I would like to be able to automatically crop that space out and leave the essentials. Original image has a squared canvas, optimally it would be rectangular, encapsulating just the molecule.

here’s the original image:
Original Image

Doing some googling i came across PIL/python code that was reported to work, however in my hands, running the code below over-crops the image.

import Image
import sys

image=Image.open('L_2d.png')
image.load()

imageSize = image.size
imageBox = image.getbbox()

imageComponents = image.split()

rgbImage = Image.new("RGB", imageSize, (0,0,0))
rgbImage.paste(image, mask=imageComponents[3])
croppedBox = rgbImage.getbbox()
print imageBox
print croppedBox
if imageBox != croppedBox:
    cropped=image.crop(croppedBox)
    print 'L_2d.png:', "Size:", imageSize, "New Size:",croppedBox
    cropped.save('L_2d_cropped.png')

the output is this:script's output

Can anyone more familiar with image-processing/PLI can help me figure out the issue?

Solution

You can use numpy, convert the image to array, find all non-empty columns and rows and then create an image from these:

import Image
import numpy as np

image=Image.open('L_2d.png')
image.load()

image_data = np.asarray(image)
image_data_bw = image_data.max(axis=2)
non_empty_columns = np.where(image_data_bw.max(axis=0)>0)[0]
non_empty_rows = np.where(image_data_bw.max(axis=1)>0)[0]
cropBox = (min(non_empty_rows), max(non_empty_rows), min(non_empty_columns), max(non_empty_columns))

image_data_new = image_data[cropBox[0]:cropBox[1]+1, cropBox[2]:cropBox[3]+1 , :]

new_image = Image.fromarray(image_data_new)
new_image.save('L_2d_cropped.png')

The result looks like
cropped image

If anything is unclear, just ask.

Answered By – Thorsten Kranz

Answer Checked By – Jay B. (AngularFixing Admin)

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