Calculating volume of 3D model in Python

Question

I have a nii file of a kidney which I upload in Python. Is there any function in itk or vtk to calculate a volume of the kidney?

Answer 1

I share with you a solution with SimpleITK.

You require a mask image of the kidney. The mask is a binary image with 1 values where the organ is and 0 values otherwise. If you don't have this already you can use 3DSlicer to segment the image, see here: 3DSlicer Segmentation. After this you will have a kidney_mask.nii (or nrrd, default format) file.

You can use the following script to compute the volume.

# script file image_volume.py
import argparse                 # argument parser
import numpy as np
import SimpleITK as sitk

def volume( mask_image ):
    # Input:
    # image = sitk.Image, mask or binary image (1 values where organ, 0 values otherwise)
    # Output:
    # vol = float, volume in mm3 
    space = mask_image.GetSpacing()         # image spacing
    voxel = np.prod(space)                  # voxel volume
    img = sitk.GetArrayFromImage(mask_image)
    vol = voxel*np.sum(img)
    return vol

def main():
    # Arguments details
    parser = argparse.ArgumentParser(description='Compute volume of a mask image')
    parser.add_argument("input", type=str, 
                        help='Input file name')

    # Parse arguments
    args = parser.parse_args()
    image_file = args.input

    # Read the image
    try:
        image = sitk.ReadImage(image_file)
    except:
        print('Unable to read input image file.')

    # Calculate the volume
    print('Volume: {:f} [mm3]'.format(volume(image)))
    print('Volume: {:f} [cm3]'.format(volume(image)/1000.0))

    return
    
if __name__ == "__main__":
    # execute only if run as a script
    main()

Call the script as:

python image_volume.py '/path/folder/kidney_mask.nii'

Answer 2

Here's how you can do it in just SimpleITK (the other answer uses numpy for the voxel count)

import SimpleITK as sitk

stats = sitk.StatisticsImageFilter()

# img is a SimpleITK image
stats.Execute(img)

# get the number of voxels with label 1
nvoxels = stats.GetCount(1)

spacing = img.GetSpacing()
voxvol = spacing[0]*spacing[1]*spacing[2]

volume = nvoxels * voxvol