Convert multiple tiff images in a directory to a single 3D nifti file

tif_to_nii.py

"""
tif_to_nii
Convert multiple tiff images in a directory to a single 3D nifti file.
Naming Convention: root001_01 - root001_100, root002_01 - root002_100, ...

Usage instructions: change the source path (src_path) [represents the path to your tiff images], 
destination path (dest_path) [represents the path you want to store your 3D nifti file in] and bases 
[this represents the name of the files] accordingly

Author: liuhh02 https://machinelearningtutorials.weebly.com/
"""
import re
import glob
import os
import nibabel as nib
from PIL import Image
# Function to sort
def sort( l ):
    """ Sort the given list in the way that humans expect."""
    convert = lambda text: int(text) if text.isdigit() else text
    alphanum_key = lambda key: [ convert(c) for c in re.split('([0-9]+)', key) ]
    l.sort( key=alphanum_key )
    return l
  
# define paths
src_path = './valid/'
dest_path = './volumes/'

# define list of base names
bases = ['root001', 'root002', 'root003']

# loop through each base
for base in bases:
# get names for the file
    names = glob.glob(src_path + base + '*.tif')
    # check all the files have been found
    print(names)
    names = sort(names)
    # check the sorting has been done correctly
    print(names)
    # check the correct number of slices have been found
    print(len(names))
    i = 0
    # create an empty 3d numpy array with the desired shape: number of slices, dimensions of each slice
    image_stacks = np.zeros(shape=(len(names), 256, 256), dtype=np.float32)
    # loop through all the files in the list and open them
    for filename in names:
        img = Image.open(filename)
        # add the slice to the 3D volume
        image_stacks[i] = np.array(img)
        i+=1
    # check shape is correct
    print(image_stacks.shape)
    # create nifti file
    nifti = nib.Nifti1Image(image_stacks, affine=np.eye(4))
    # define filename
    out_fn = os.path.join(dest_path, base + '.nii.gz')
    nifti.to_filename(out_fn)
    print("Saved", out_fn)