From d7c706975e8fc8c6a2fac9d83c2f006c236b4c6c Mon Sep 17 00:00:00 2001
From: Julian Klug <tensu.wave@gmail.com>
Date: Wed, 9 Sep 2020 23:52:38 +0200
Subject: [PATCH 1/9] Added a volume computation function
Compute volume of mask image.
Equivalent to "fslstats /path/file.nii -V"
---
nibabel/funcs.py | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)
diff --git a/nibabel/funcs.py b/nibabel/funcs.py
index df5eb0e96f..37eda9d66e 100644
--- a/nibabel/funcs.py
+++ b/nibabel/funcs.py
@@ -215,3 +215,34 @@ def _aff_is_diag(aff):
""" Utility function returning True if affine is nearly diagonal """
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
From 73bff0ff6742ae4e4e04f33dcbe64f6d710f98ae Mon Sep 17 00:00:00 2001
From: Julian Klug <tensu.wave@gmail.com>
Date: Sun, 18 Oct 2020 10:20:45 +0300
Subject: [PATCH 2/9] Added commandline and tests for imagestats volume
computation
---
bin/nib-stats.py | 18 +++++++++
nibabel/cmdline/stats.py | 39 ++++++++++++++++++++
nibabel/cmdline/tests/test_stats.py | 33 +++++++++++++++++
nibabel/funcs.py | 30 ---------------
nibabel/imagestats.py | 57 +++++++++++++++++++++++++++++
nibabel/tests/test_imagestats.py | 29 +++++++++++++++
6 files changed, 176 insertions(+), 30 deletions(-)
create mode 100644 bin/nib-stats.py
create mode 100644 nibabel/cmdline/stats.py
create mode 100644 nibabel/cmdline/tests/test_stats.py
create mode 100644 nibabel/imagestats.py
create mode 100644 nibabel/tests/test_imagestats.py
diff --git a/bin/nib-stats.py b/bin/nib-stats.py
new file mode 100644
index 0000000000..4544b415aa
--- /dev/null
+++ b/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()
diff --git a/nibabel/cmdline/stats.py b/nibabel/cmdline/stats.py
new file mode 100644
index 0000000000..81aded8041
--- /dev/null
+++ b/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
diff --git a/nibabel/cmdline/tests/test_stats.py b/nibabel/cmdline/tests/test_stats.py
new file mode 100644
index 0000000000..4fa8a14094
--- /dev/null
+++ b/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
+
+
diff --git a/nibabel/funcs.py b/nibabel/funcs.py
index 37eda9d66e..e12acee57d 100644
--- a/nibabel/funcs.py
+++ b/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
diff --git a/nibabel/imagestats.py b/nibabel/imagestats.py
new file mode 100644
index 0000000000..c6b855ae8e
--- /dev/null
+++ b/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".')
diff --git a/nibabel/tests/test_imagestats.py b/nibabel/tests/test_imagestats.py
new file mode 100644
index 0000000000..918bf38fc3
--- /dev/null
+++ b/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
+
From 57f7723ca46d964e710ad5cefbf2bcd40c096563 Mon Sep 17 00:00:00 2001
From: Julian Klug <tensu.wave@gmail.com>
Date: Sun, 18 Oct 2020 10:41:02 +0300
Subject: [PATCH 3/9] Fix style errors - blank lines - variable declaration in
example
---
nibabel/imagestats.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/nibabel/imagestats.py b/nibabel/imagestats.py
index c6b855ae8e..1877c1fff4 100644
--- a/nibabel/imagestats.py
+++ b/nibabel/imagestats.py
@@ -38,6 +38,7 @@ def mask_volume(img, units='mm3'):
Examples
--------
>>> import nibabel as nf
+ >>> path = 'path/to/nifti/mask.nii'
>>> img = nf.load(path) # path is contains a path to an example nifti mask
>>> mask_volume(img)
50.3021
From e15bb8d1c43ca6d20996bcbd022195b7a77029c7 Mon Sep 17 00:00:00 2001
From: Julian Klug <tensu.wave@gmail.com>
Date: Sun, 18 Oct 2020 19:43:34 +0200
Subject: [PATCH 4/9] Apply suggestions from code review: Removing unused code
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
nibabel/cmdline/stats.py | 4 ++--
nibabel/cmdline/tests/test_stats.py | 9 ---------
2 files changed, 2 insertions(+), 11 deletions(-)
diff --git a/nibabel/cmdline/stats.py b/nibabel/cmdline/stats.py
index 81aded8041..e7e4348003 100644
--- a/nibabel/cmdline/stats.py
+++ b/nibabel/cmdline/stats.py
@@ -24,7 +24,7 @@ def _get_parser():
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")
+ choices=("mm3", "vox"), help="Preferred output units")
return p
def main(args=None):
@@ -36,4 +36,4 @@ def main(args=None):
if opts.Volume:
computed_volume = mask_volume(from_img, opts.units)
print(computed_volume)
- return computed_volume
+ return 0
diff --git a/nibabel/cmdline/tests/test_stats.py b/nibabel/cmdline/tests/test_stats.py
index 4fa8a14094..dd14044486 100644
--- a/nibabel/cmdline/tests/test_stats.py
+++ b/nibabel/cmdline/tests/test_stats.py
@@ -8,16 +8,8 @@
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-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():
@@ -30,4 +22,3 @@ def test_volume():
assert float(vol_mm3) == 2273328656.0
assert float(vol_vox) == 284166082.0
-
From 7412ba9789d431297ddee02db4403aa14bd57d2d Mon Sep 17 00:00:00 2001
From: Julian Klug <tensu.wave@gmail.com>
Date: Sun, 18 Oct 2020 19:55:12 +0200
Subject: [PATCH 5/9] Apply suggestions from code review: Use header.get_zooms
instead of header.pixdim
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
nibabel/imagestats.py | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/nibabel/imagestats.py b/nibabel/imagestats.py
index 1877c1fff4..9b4356ca8a 100644
--- a/nibabel/imagestats.py
+++ b/nibabel/imagestats.py
@@ -11,6 +11,7 @@
"""
import numpy as np
+from nibabel.imageclasses import spatial_axes_first
def mask_volume(img, units='mm3'):
@@ -43,11 +44,10 @@ def mask_volume(img, units='mm3'):
>>> 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)
+ 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 = np.count_nonzero(img.dataobj)
mask_volume_mm3 = mask_volume_vx * voxel_volume_mm3
if units == 'vox':
From d357eae8d70d53f0f6c2d41265fafc38a3cbac17 Mon Sep 17 00:00:00 2001
From: Julian Klug <tensu.wave@gmail.com>
Date: Mon, 19 Oct 2020 01:11:02 +0300
Subject: [PATCH 6/9] Split Mask_volume into a function for voxels and a
function for volume in mm3 - use a mask-like volume for testing
---
nibabel/cmdline/stats.py | 9 ++++--
nibabel/cmdline/tests/test_stats.py | 39 ++++++++++++++++++++------
nibabel/imagestats.py | 43 +++++++++++++++--------------
nibabel/tests/test_imagestats.py | 16 ++++++-----
setup.cfg | 1 +
5 files changed, 71 insertions(+), 37 deletions(-)
diff --git a/nibabel/cmdline/stats.py b/nibabel/cmdline/stats.py
index e7e4348003..0ea4617936 100644
--- a/nibabel/cmdline/stats.py
+++ b/nibabel/cmdline/stats.py
@@ -13,7 +13,7 @@
import argparse
from nibabel.loadsave import load
-from nibabel.imagestats import mask_volume
+from nibabel.imagestats import mask_volume, count_nonzero_voxels
def _get_parser():
@@ -34,6 +34,11 @@ def main(args=None):
from_img = load(opts.infile)
if opts.Volume:
- computed_volume = mask_volume(from_img, opts.units)
+ 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
diff --git a/nibabel/cmdline/tests/test_stats.py b/nibabel/cmdline/tests/test_stats.py
index dd14044486..2a3e43a4d5 100644
--- a/nibabel/cmdline/tests/test_stats.py
+++ b/nibabel/cmdline/tests/test_stats.py
@@ -8,17 +8,40 @@
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-from nibabel.testing import test_data
+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
+
+
+class Capturing(list):
+ def __enter__(self):
+ self._stdout = sys.stdout
+ sys.stdout = self._stringio = StringIO()
+ return self
+ def __exit__(self, *args):
+ self.extend(self._stringio.getvalue().splitlines())
+ del self._stringio # free up some memory
+ sys.stdout = self._stdout
-def test_volume():
- infile = test_data(fname="anatomical.nii")
+def test_volume(tmpdir):
+ 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")
- vol_mm3 = main(args.split())
+ with Capturing() as 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
+ with Capturing() as vol_vox:
+ main(args.split())
+ assert float(vol_mm3[0]) == 1000.0
+ assert int(vol_vox[0]) == 1000
\ No newline at end of file
diff --git a/nibabel/imagestats.py b/nibabel/imagestats.py
index 9b4356ca8a..20422fee54 100644
--- a/nibabel/imagestats.py
+++ b/nibabel/imagestats.py
@@ -13,8 +13,23 @@
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
+ -------
+ non zero voxel volume: int
+ Number of non-zero voxels
+
+ """
+ return np.count_nonzero(img.dataobj)
-def mask_volume(img, units='mm3'):
+def mask_volume(img):
""" Compute volume of mask image.
Equivalent to "fslstats /path/file.nii -V"
@@ -23,36 +38,24 @@ def mask_volume(img, units='mm3'):
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
- >>> path = 'path/to/nifti/mask.nii'
- >>> img = nf.load(path) # path is contains a path to an example nifti mask
- >>> mask_volume(img)
- 50.3021
+ >>> 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 = np.count_nonzero(img.dataobj)
+ mask_volume_vx = count_nonzero_voxels(img)
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".')
+ return mask_volume_mm3
diff --git a/nibabel/tests/test_imagestats.py b/nibabel/tests/test_imagestats.py
index 918bf38fc3..d8ef2018c1 100644
--- a/nibabel/tests/test_imagestats.py
+++ b/nibabel/tests/test_imagestats.py
@@ -11,19 +11,21 @@
import numpy as np
from .. import imagestats
-from nibabel.testing import test_data
-from nibabel.loadsave import load
+from .. import Nifti1Image
import pytest
def test_mask_volume():
# Test mask volume computation
- infile = test_data(fname="anatomical.nii")
- img = load(infile)
+
+ 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.mask_volume(img, units='vox')
+ vol_vox = imagestats.count_nonzero_voxels(img)
- assert float(vol_mm3) == 2273328656.0
- assert float(vol_vox) == 284166082.0
+ assert vol_mm3 == 1000.0
+ assert vol_vox == 1000
diff --git a/setup.cfg b/setup.cfg
index c2bf604f94..141a37caec 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -73,6 +73,7 @@ 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
From 93532dedbb547597bbc29444bd67e5068b5a9752 Mon Sep 17 00:00:00 2001
From: Julian Klug <tensu.wave@gmail.com>
Date: Mon, 19 Oct 2020 09:12:41 +0300
Subject: [PATCH 7/9] Fix failing docstring
---
nibabel/imagestats.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/nibabel/imagestats.py b/nibabel/imagestats.py
index 20422fee54..74506a07ff 100644
--- a/nibabel/imagestats.py
+++ b/nibabel/imagestats.py
@@ -46,10 +46,11 @@ def mask_volume(img):
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))
+ >>> nb.imagestats.mask_volume(nb.Nifti1Image(mask_data, np.eye(4)))
1000.0
"""
if not spatial_axes_first(img):
From 2331e9d33677cb7fb14eec84d925b7dd18cce740 Mon Sep 17 00:00:00 2001
From: Julian Klug <tensu.wave@gmail.com>
Date: Mon, 19 Oct 2020 22:10:13 +0200
Subject: [PATCH 8/9] Apply suggestions from code review
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
nibabel/imagestats.py | 6 ++++--
nibabel/tests/test_imagestats.py | 3 ---
2 files changed, 4 insertions(+), 5 deletions(-)
diff --git a/nibabel/imagestats.py b/nibabel/imagestats.py
index 74506a07ff..3af2d8a089 100644
--- a/nibabel/imagestats.py
+++ b/nibabel/imagestats.py
@@ -16,6 +16,7 @@
def count_nonzero_voxels(img):
"""
Count number of non-zero voxels
+
Parameters
----------
img : ``SpatialImage``
@@ -23,7 +24,7 @@ def count_nonzero_voxels(img):
Returns
-------
- non zero voxel volume: int
+ count : int
Number of non-zero voxels
"""
@@ -31,6 +32,7 @@ def count_nonzero_voxels(img):
def mask_volume(img):
""" Compute volume of mask image.
+
Equivalent to "fslstats /path/file.nii -V"
Parameters
@@ -41,7 +43,7 @@ def mask_volume(img):
Returns
-------
- mask_volume_mm3: float
+ volume : float
Volume of mask expressed in mm3.
Examples
diff --git a/nibabel/tests/test_imagestats.py b/nibabel/tests/test_imagestats.py
index d8ef2018c1..e104013ddd 100644
--- a/nibabel/tests/test_imagestats.py
+++ b/nibabel/tests/test_imagestats.py
@@ -13,8 +13,6 @@
from .. import imagestats
from .. import Nifti1Image
-import pytest
-
def test_mask_volume():
# Test mask volume computation
@@ -28,4 +26,3 @@ def test_mask_volume():
assert vol_mm3 == 1000.0
assert vol_vox == 1000
-
From 35beabab98e6ab2a924fd91055c70277bf91cf7b Mon Sep 17 00:00:00 2001
From: Julian Klug <tensu.wave@gmail.com>
Date: Tue, 20 Oct 2020 00:34:49 +0300
Subject: [PATCH 9/9] Style issues, use capsys
---
bin/nib-stats.py | 18 ------------------
nibabel/cmdline/stats.py | 1 +
nibabel/cmdline/tests/test_stats.py | 21 +++++----------------
nibabel/funcs.py | 1 -
nibabel/imagestats.py | 2 ++
5 files changed, 8 insertions(+), 35 deletions(-)
delete mode 100644 bin/nib-stats.py
diff --git a/bin/nib-stats.py b/bin/nib-stats.py
deleted file mode 100644
index 4544b415aa..0000000000
--- a/bin/nib-stats.py
+++ /dev/null
@@ -1,18 +0,0 @@
-#!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()
diff --git a/nibabel/cmdline/stats.py b/nibabel/cmdline/stats.py
index 0ea4617936..91b9f7c104 100644
--- a/nibabel/cmdline/stats.py
+++ b/nibabel/cmdline/stats.py
@@ -27,6 +27,7 @@ def _get_parser():
choices=("mm3", "vox"), help="Preferred output units")
return p
+
def main(args=None):
"""Main program function."""
parser = _get_parser()
diff --git a/nibabel/cmdline/tests/test_stats.py b/nibabel/cmdline/tests/test_stats.py
index 2a3e43a4d5..1ceac90231 100644
--- a/nibabel/cmdline/tests/test_stats.py
+++ b/nibabel/cmdline/tests/test_stats.py
@@ -17,18 +17,7 @@
from nibabel import Nifti1Image
-class Capturing(list):
- def __enter__(self):
- self._stdout = sys.stdout
- sys.stdout = self._stringio = StringIO()
- return self
- def __exit__(self, *args):
- self.extend(self._stringio.getvalue().splitlines())
- del self._stringio # free up some memory
- sys.stdout = self._stdout
-
-
-def test_volume(tmpdir):
+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))
@@ -37,11 +26,11 @@ def test_volume(tmpdir):
save(img, infile)
args = (f"{infile} --Volume")
- with Capturing() as vol_mm3:
- main(args.split())
+ main(args.split())
+ vol_mm3 = capsys.readouterr()
args = (f"{infile} --Volume --units vox")
- with Capturing() as vol_vox:
- main(args.split())
+ main(args.split())
+ vol_vox = capsys.readouterr()
assert float(vol_mm3[0]) == 1000.0
assert int(vol_vox[0]) == 1000
\ No newline at end of file
diff --git a/nibabel/funcs.py b/nibabel/funcs.py
index e12acee57d..df5eb0e96f 100644
--- a/nibabel/funcs.py
+++ b/nibabel/funcs.py
@@ -215,4 +215,3 @@ def _aff_is_diag(aff):
""" Utility function returning True if affine is nearly diagonal """
rzs_aff = aff[:3, :3]
return np.allclose(rzs_aff, np.diag(np.diag(rzs_aff)))
-
diff --git a/nibabel/imagestats.py b/nibabel/imagestats.py
index 3af2d8a089..4520d7f612 100644
--- a/nibabel/imagestats.py
+++ b/nibabel/imagestats.py
@@ -13,6 +13,7 @@
import numpy as np
from nibabel.imageclasses import spatial_axes_first
+
def count_nonzero_voxels(img):
"""
Count number of non-zero voxels
@@ -30,6 +31,7 @@ def count_nonzero_voxels(img):
"""
return np.count_nonzero(img.dataobj)
+
def mask_volume(img):
""" Compute volume of mask image.