Python function to create maximum intensity projections using SimpleITK

README.md

Requirements:

• Python
• SimpleITK
• NumPy

Install

• conda
• SimpleITK and NumPy:

conda install numpy -y
conda install -c simpleitk simpleitk -y

mip.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Fri Nov 10 16:51:47 2017

@author: fernando
"""

import os

import numpy as np
import SimpleITK as sitk

def make_mips(image_path, output_dir):
    image = sitk.ReadImage(image_path)
    image_size = image.GetSize()

    basename = os.path.basename(image_path)
    if not os.path.isdir(output_dir):
        os.makedirs(output_dir)

    for dim in range(3):
        projection = sitk.MaximumProjection(image, dim)

        if image_size[dim] % 2:  # odd number
            voxel = [0, 0, 0]
            voxel[dim] = (image_size[dim] - 1) / 2
            origin = image.TransformIndexToPhysicalPoint(voxel)
        else:  # even
            voxel1 = np.array([0, 0, 0], int)
            voxel2 = np.array([0, 0, 0], int)
            voxel1[dim] = image_size[dim] / 2 - 1
            voxel2[dim] = image_size[dim] / 2
            point1 = np.array(image.TransformIndexToPhysicalPoint(voxel1.tolist()))
            point2 = np.array(image.TransformIndexToPhysicalPoint(voxel2.tolist()))
            origin = np.mean(np.vstack((point1, point2)), 0)
        projection.SetOrigin(origin)
        projection.SetDirection(image.GetDirection())
        proj_basename = basename.replace('.nii.gz', '_mip_{}.nii.gz'.format(dim))
        sitk.WriteImage(projection, os.path.join(output_dir, proj_basename))