Python Quick Tip #4: Batching Over Files in a Directory

TL;DR

Here is the full script to load all PNGs in a given folder, convert them to 8bit grayscale TIFF, then save them to a different folder:

import os
from skimage import io
from skimage.util import img_as_ubyte

# You need to change these to valid directories on your computer
input_dir = os.path.dirname('C:/FILES/leaves/')
output_dir = os.path.dirname('C:/FILES/leaves converted/')

for f in os.listdir(input_dir):
    if f.lower().endswith('.png') is True:
        image_gray = io.imread(os.path.join(input_dir, f),
                               as_gray=True)
        image_gray = img_as_ubyte(image_gray)
        output_file = f.replace('.png', '_gray.tiff')
        io.imsave(os.path.join(output_dir, output_file), image_gray)

You can also access this script on our GitHub.

Line by Line

Let's import the functionality we’ll need:

import os
from skimage import io
from skimage.util import img_as_ubyte

Let’s set the paths to the input and output file folders we’re using as variables for easy access. My input files are in a folder at C:/FILES/leaves/, and I have an empty folder at C:/FILES/leaves converted/ for the output. The os.path submodule helps ensure that code to work with paths will w