Merge pull request #952 from JulianKlug/patch-1

NF: volume computation function for nifti masks

Author: effigies

nibabel/cmdline/stats.py

@@ -0,0 +1,45 @@
+#!python
+# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+#
+#   See COPYING file distributed along with the NiBabel package for the
+#   copyright and license terms.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+"""
+Compute image statistics
+"""
+
+import argparse
+from nibabel.loadsave import load
+from nibabel.imagestats import mask_volume, count_nonzero_voxels
+
+
+def _get_parser():
+    """Return command-line argument parser."""
+    p = argparse.ArgumentParser(description=__doc__)
+    p.add_argument("infile",
+                   help="Neuroimaging volume to compute statistics on.")
+    p.add_argument("-V", "--Volume", action="store_true", required=False,
+                   help="Compute mask volume of a given mask image.")
+    p.add_argument("--units", default="mm3", required=False,
+                   choices=("mm3", "vox"), help="Preferred output units")
+    return p
+
+
+def main(args=None):
+    """Main program function."""
+    parser = _get_parser()
+    opts = parser.parse_args(args)
+    from_img = load(opts.infile)
+
+    if opts.Volume:
+        if opts.units == 'mm3':
+            computed_volume = mask_volume(from_img)
+        elif opts.units == 'vox':
+            computed_volume = count_nonzero_voxels(from_img)
+        else:
+            raise ValueError(f'{opts.units} is not a valid unit. Choose "mm3" or "vox".')
+        print(computed_volume)
+        return 0

nibabel/cmdline/tests/test_stats.py

@@ -0,0 +1,36 @@
+#!python
+# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+#
+#   See COPYING file distributed along with the NiBabel package for the
+#   copyright and license terms.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+
+from io import StringIO
+import sys
+import numpy as np
+
+from nibabel.loadsave import save
+from nibabel.cmdline.stats import main
+from nibabel import Nifti1Image
+
+
+def test_volume(tmpdir, capsys):
+    mask_data = np.zeros((20, 20, 20), dtype='u1')
+    mask_data[5:15, 5:15, 5:15] = 1
+    img = Nifti1Image(mask_data, np.eye(4))
+
+    infile = tmpdir / "input.nii"
+    save(img, infile)
+
+    args = (f"{infile} --Volume")
+    main(args.split())
+    vol_mm3 = capsys.readouterr()
+    args = (f"{infile} --Volume --units vox")
+    main(args.split())
+    vol_vox = capsys.readouterr()
+
+    assert float(vol_mm3[0]) == 1000.0
+    assert int(vol_vox[0]) == 1000

nibabel/imagestats.py

@@ -0,0 +1,66 @@
+# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+#
+#   See COPYING file distributed along with the NiBabel package for the
+#   copyright and license terms.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+"""
+Functions for computing image statistics
+"""
+
+import numpy as np
+from nibabel.imageclasses import spatial_axes_first
+
+
+def count_nonzero_voxels(img):
+    """
+    Count number of non-zero voxels
+
+    Parameters
+    ----------
+    img : ``SpatialImage``
+        All voxels of the mask should be of value 1, background should have value 0.
+
+    Returns
+    -------
+    count : int
+        Number of non-zero voxels
+
+    """
+    return np.count_nonzero(img.dataobj)
+
+
+def mask_volume(img):
+    """ Compute volume of mask image.
+
+    Equivalent to "fslstats /path/file.nii -V"
+
+    Parameters
+    ----------
+    img : ``SpatialImage``
+        All voxels of the mask should be of value 1, background should have value 0.
+
+
+    Returns
+    -------
+    volume : float
+        Volume of mask expressed in mm3.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> import nibabel as nb
+    >>> mask_data = np.zeros((20, 20, 20), dtype='u1')
+    >>> mask_data[5:15, 5:15, 5:15] = 1
+    >>> nb.imagestats.mask_volume(nb.Nifti1Image(mask_data, np.eye(4)))
+    1000.0
+    """
+    if not spatial_axes_first(img):
+        raise ValueError("Cannot calculate voxel volume for image with unknown spatial axes")
+    voxel_volume_mm3 = np.prod(img.header.get_zooms()[:3])
+    mask_volume_vx = count_nonzero_voxels(img)
+    mask_volume_mm3 = mask_volume_vx * voxel_volume_mm3
+
+    return mask_volume_mm3

nibabel/tests/test_imagestats.py

@@ -0,0 +1,28 @@
+# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+#
+#   See COPYING file distributed along with the NiBabel package for the
+#   copyright and license terms.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+""" Tests for image statistics """
+
+import numpy as np
+
+from .. import imagestats
+from .. import Nifti1Image
+
+
+def test_mask_volume():
+    # Test mask volume computation
+
+    mask_data = np.zeros((20, 20, 20), dtype='u1')
+    mask_data[5:15, 5:15, 5:15] = 1
+    img = Nifti1Image(mask_data, np.eye(4))
+
+    vol_mm3 = imagestats.mask_volume(img)
+    vol_vox = imagestats.count_nonzero_voxels(img)
+
+    assert vol_mm3 == 1000.0
+    assert vol_vox == 1000

setup.cfg

@@ -74,6 +74,7 @@ console_scripts =
     nib-ls=nibabel.cmdline.ls:main
     nib-dicomfs=nibabel.cmdline.dicomfs:main
     nib-diff=nibabel.cmdline.diff:main
+    nib-stats=nibabel.cmdline.stats:main
     nib-nifti-dx=nibabel.cmdline.nifti_dx:main
     nib-tck2trk=nibabel.cmdline.tck2trk:main
     nib-trk2tck=nibabel.cmdline.trk2tck:main