Added commandline and tests for imagestats volume computation

Author: JulianKlug

bin/nib-stats.py

@@ -0,0 +1,18 @@
+#!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
+"""
+
+from nibabel.cmdline.stats import main
+
+
+if __name__ == '__main__':
+    main()

nibabel/cmdline/stats.py

@@ -0,0 +1,39 @@
+#!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
+
+
+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,
+                   help="Preferred output units of {mm3, vox}. Defaults to mm3")
+    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:
+        computed_volume = mask_volume(from_img, opts.units)
+        print(computed_volume)
+        return computed_volume

nibabel/cmdline/tests/test_stats.py

@@ -0,0 +1,33 @@
+#!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.
+#
+### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
+
+import unittest
+
+import pytest
+
+from nibabel.testing import test_data
+from nibabel.cmdline.stats import main
+from nibabel.optpkg import optional_package
+
+_, have_scipy, _ = optional_package('scipy.ndimage')
+needs_scipy = unittest.skipUnless(have_scipy, 'These tests need scipy')
+
+
+def test_volume():
+    infile = test_data(fname="anatomical.nii")
+    args = (f"{infile} --Volume")
+    vol_mm3 = main(args.split())
+    args = (f"{infile} --Volume --units vox")
+    vol_vox = main(args.split())
+
+    assert float(vol_mm3) == 2273328656.0
+    assert float(vol_vox) == 284166082.0
+
+

nibabel/funcs.py

@@ -216,33 +216,3 @@ def _aff_is_diag(aff):
     rzs_aff = aff[:3, :3]
     return np.allclose(rzs_aff, np.diag(np.diag(rzs_aff)))
 
-
-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
-    -------
-    mask_volume_mm3: float
-        Volume of mask expressed in mm3.
-
-    Examples
-    --------
-    >>> import nibabel as nf
-    >>> img = nf.load(path) # path is contains a path to an example nifti mask
-    >>> mask_volume(img)
-    50.3021
-    """
-    header = img.header
-    _, vx, vy, vz, _, _, _, _ = header['pixdim']
-    voxel_volume_mm3 = vx * vy * vz
-    mask = img.get_fdata()
-    mask_volume_vx = np.sum(mask)
-    mask_volume_mm3 = mask_volume_vx * voxel_volume_mm3
-
-    return mask_volume_mm3

nibabel/imagestats.py

@@ -0,0 +1,57 @@
+# 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
+
+
+def mask_volume(img, units='mm3'):
+    """ 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.
+
+    units : string {"mm3", "vox"}, optional
+        Unit of the returned mask volume. Defaults to "mm3".
+
+    Returns
+    -------
+    mask_volume_vx: float
+        Volume of mask expressed in voxels.
+
+    or
+
+    mask_volume_mm3: float
+        Volume of mask expressed in mm3.
+
+    Examples
+    --------
+    >>> import nibabel as nf
+    >>> img = nf.load(path) # path is contains a path to an example nifti mask
+    >>> mask_volume(img)
+    50.3021
+    """
+    header = img.header
+    _, vx, vy, vz, _, _, _, _ = header['pixdim']
+    voxel_volume_mm3 = vx * vy * vz
+    mask = img.get_fdata()
+    mask_volume_vx = np.sum(mask)
+    mask_volume_mm3 = mask_volume_vx * voxel_volume_mm3
+
+    if units == 'vox':
+        return mask_volume_vx
+    elif units == 'mm3':
+        return mask_volume_mm3
+    else:
+        raise ValueError(f'{units} is not a valid unit. Choose "mm3" or "vox".')

nibabel/tests/test_imagestats.py

@@ -0,0 +1,29 @@
+# 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 nibabel.testing import test_data
+from nibabel.loadsave import load
+
+import pytest
+
+
+def test_mask_volume():
+    # Test mask volume computation
+    infile = test_data(fname="anatomical.nii")
+    img = load(infile)
+    vol_mm3 = imagestats.mask_volume(img)
+    vol_vox = imagestats.mask_volume(img, units='vox')
+
+    assert float(vol_mm3) == 2273328656.0
+    assert float(vol_vox) == 284166082.0
+