jcreinhold/tif_to_nii.py

## tif_to_nii.py
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
tif_to_nii

command line executable to convert a directory of tif images
(from one image) to a nifti image stacked along a user-specified axis

call as: python tif_to_nii.py /path/to/tif/ /path/to/nifti
(append optional arguments to the call as desired)

Author: Jacob Reinhold (jacob.reinhold@jhu.edu)
"""

import argparse
from glob import glob
import os
from pathlib import Path
import sys

from PIL import Image
import nibabel as nib
import numpy as np


def arg_parser():
    parser = argparse.ArgumentParser(description='merge 2d tif images into a 3d image')
    parser.add_argument('img_dir', type=str,
                        help='path to tiff image directory')
    parser.add_argument('out_dir', type=str,
                        help='path to output the corresponding tif image slices')
    parser.add_argument('-a', '--axis', type=int, default=2,
                        help='axis on which to stack the 2d images')
    return parser


def split_filename(filepath):
    path = os.path.dirname(filepath)
    filename = os.path.basename(filepath)
    base, ext = os.path.splitext(filename)
    if ext == '.gz':
        base, ext2 = os.path.splitext(base)
        ext = ext2 + ext
    return path, base, ext


def main():
    try:
        args = arg_parser().parse_args()
        img_dir = Path(args.img_dir)
        fns = sorted([str(fn) for fn in img_dir.glob('*.tif*')])
        if not fns:
            raise ValueError(f'img_dir ({args.img_dir}) does not contain any .tif or .tiff images.')
        imgs = []
        for fn in fns:
            _, base, ext = split_filename(fn)
            img = np.asarray(Image.open(fn)).astype(np.float32).squeeze()
            if img.ndim != 2:
                raise Exception(f'Only 2D data supported. File {base}{ext} has dimension {img.ndim}.')
            imgs.append(img)
        img = np.stack(imgs, axis=args.axis)
        nib.Nifti1Image(img,None).to_filename(os.path.join(args.out_dir, f'{base}.nii.gz'))
        return 0
    except Exception as e:
        print(e)
        return 1


if __name__ == "__main__":
    sys.exit(main())
	#!/usr/bin/env python
	# -- coding: utf-8 --
	"""
	tif_to_nii

	command line executable to convert a directory of tif images
	(from one image) to a nifti image stacked along a user-specified axis

	call as: python tif_to_nii.py /path/to/tif/ /path/to/nifti
	(append optional arguments to the call as desired)

	Author: Jacob Reinhold (jacob.reinhold@jhu.edu)
	"""

	import argparse
	from glob import glob
	import os
	from pathlib import Path
	import sys

	from PIL import Image
	import nibabel as nib
	import numpy as np


	def arg_parser():
	parser = argparse.ArgumentParser(description='merge 2d tif images into a 3d image')
	parser.add_argument('img_dir', type=str,
	help='path to tiff image directory')
	parser.add_argument('out_dir', type=str,
	help='path to output the corresponding tif image slices')
	parser.add_argument('-a', '--axis', type=int, default=2,
	help='axis on which to stack the 2d images')
	return parser


	def split_filename(filepath):
	path = os.path.dirname(filepath)
	filename = os.path.basename(filepath)
	base, ext = os.path.splitext(filename)
	if ext == '.gz':
	base, ext2 = os.path.splitext(base)
	ext = ext2 + ext
	return path, base, ext


	def main():
	try:
	args = arg_parser().parse_args()
	img_dir = Path(args.img_dir)
	fns = sorted([str(fn) for fn in img_dir.glob('.tif')])
	if not fns:
	raise ValueError(f'img_dir ({args.img_dir}) does not contain any .tif or .tiff images.')
	imgs = []
	for fn in fns:
	_, base, ext = split_filename(fn)
	img = np.asarray(Image.open(fn)).astype(np.float32).squeeze()
	if img.ndim != 2:
	raise Exception(f'Only 2D data supported. File {base}{ext} has dimension {img.ndim}.')
	imgs.append(img)
	img = np.stack(imgs, axis=args.axis)
	nib.Nifti1Image(img,None).to_filename(os.path.join(args.out_dir, f'{base}.nii.gz'))
	return 0
	except Exception as e:
	print(e)
	return 1


	if __name__ == "__main__":
	sys.exit(main())