NF: volume computation function for nifti masks #952

JulianKlug · 2020-09-09T21:58:35Z

Adds a function to compute the volume of a mask image in mm3.
Simple vanilla python equivalent to "fslstats /path/file.nii -V".

Reason: Useful for pure python projects where one can not rely on fsl.

To Do:

Add CLI

Compute volume of mask image. Equivalent to "fslstats /path/file.nii -V"

JulianKlug · 2020-09-09T22:00:11Z

A few questions to help me guide this PR:

Would this be the right location for this function? As I am still new to the source code of nibabel, I was unsure on where to add it.
Where should the CLI for this function be?

codecov · 2020-09-09T22:06:28Z

Codecov Report

Merging #952 into master will increase coverage by 0.04%.
The diff coverage is 85.29%.

@@            Coverage Diff             @@
##           master     #952      +/-   ##
==========================================
+ Coverage   91.84%   91.89%   +0.04%     
==========================================
  Files          97      101       +4     
  Lines       12428    12548     +120     
  Branches     2191     2208      +17     
==========================================
+ Hits        11415    11531     +116     
- Misses        678      680       +2     
- Partials      335      337       +2

Impacted Files	Coverage Δ
nibabel/imagestats.py	`83.33% <83.33%> (ø)`
nibabel/cmdline/stats.py	`86.36% <86.36%> (ø)`
nibabel/testing/__init__.py	`99.05% <0.00%> (-0.95%)`	⬇️
nibabel/loadsave.py	`92.59% <0.00%> (ø)`
nibabel/deprecator.py	`100.00% <0.00%> (ø)`
nibabel/cmdline/roi.py	`100.00% <0.00%> (ø)`
nibabel/conftest.py	`100.00% <0.00%> (ø)`
nibabel/casting.py	`86.32% <0.00%> (+0.17%)`	⬆️
... and 1 more

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0rC0 · 2020-09-10T11:12:17Z

I think you've forgot a return :P, something like:

return mask_volume_vx * voxel_volume_mm3

or

return mask_volume_mm3

effigies · 2020-09-10T13:06:49Z

If we want to implement something equivalent to fslstats, then I think it might be worth creating nibabel.imagestats (I think nibabel.stats might imply more analytical statistics, which are covered in nilearn) as a place to house the various functions.

The command line should be in nibabel.cmdline.<tool>, and expose the entrypoint nib-<tool>.

JulianKlug · 2020-09-10T14:40:59Z

I think you've forgot a return :P, something like:

@0rC0 actually there is a return on line 248, it is just hidden by the codecov messages.

    return mask_volume_mm3

JulianKlug · 2020-09-10T14:42:55Z

If we want to implement something equivalent to fslstats, then I think it might be worth creating nibabel.imagestats (I think nibabel.stats might imply more analytical statistics, which are covered in nilearn) as a place to house the various functions.

The command line should be in nibabel.cmdline.<tool>, and expose the entrypoint nib-<tool>.

@effigies : Sounds good to me as well. But do you think every element of fslstats should be implemented with a single release or should we implement them gradually?

effigies · 2020-09-10T14:53:37Z

I think gradually is fine. Let's call it nib-stats and start with volume calculation.

Also, don't feel compelled to mimic the fslstats flags or output conventions exactly. Clarity is a better goal.

One thing to consider: fslstats produces both voxel and mm^3 results. Do we want to follow that lead, or permit users to say --units {vox,mm3}?

pep8speaks · 2020-10-18T07:22:50Z

Hello @JulianKlug, Thank you for updating!

Cheers! There are no style issues detected in this Pull Request. 🍻 To test for issues locally, pip install flake8 and then run flake8 nibabel.

Comment last updated at 2020-10-19 21:36:20 UTC

- blank lines - variable declaration in example

JulianKlug · 2020-10-18T08:27:39Z

There seems to be an issue where the example part of the docstring is interpreted as code and not as a string which then lets the tests fail.

    >>> path = 'path/to/nifti/mask.nii'
    >>> img = nf.load(path) # path is contains a path to an example nifti mask
    >>> mask_volume(img)

Not quite sure how to resolve this...

JulianKlug · 2020-10-18T10:13:55Z

would be ready for #960 if the aforementioned issue is resolved

effigies

Thanks for pushing on this. I've left a batch of comments. Feel free to argue and ask questions. :-)

nibabel/cmdline/tests/test_stats.py

nibabel/imagestats.py

effigies · 2020-10-18T13:00:39Z

nibabel/tests/test_imagestats.py

+    assert float(vol_mm3) == 2273328656.0
+    assert float(vol_vox) == 284166082.0


$ fslstats nibabel/tests/data/anatomical.nii -V 33825 270600.000000

I'm guessing (but haven't checked) the discrepancy is from values > 1.

I thought so too, but hadn't time to check.
The volume computation is only reliable for 0-1 masks, but as I didn't find any in the sample data, I didn’t use one for the test.

nibabel/cmdline/stats.py

effigies · 2020-10-18T13:04:50Z

bin/nib-stats.py

+
+
+if __name__ == '__main__':
+    main()


These files are actually out-of-date. Just add an entry to the entry points:

nibabel/setup.cfg

Lines 71 to 81 in 917afab

[options.entry_points]

console_scripts =

nib-conform=nibabel.cmdline.conform:main

nib-ls=nibabel.cmdline.ls:main

nib-dicomfs=nibabel.cmdline.dicomfs:main

nib-diff=nibabel.cmdline.diff:main

nib-nifti-dx=nibabel.cmdline.nifti_dx:main

nib-tck2trk=nibabel.cmdline.tck2trk:main

nib-trk2tck=nibabel.cmdline.trk2tck:main

nib-roi=nibabel.cmdline.roi:main

parrec2nii=nibabel.cmdline.parrec2nii:main

Great hadn't seen that!

Let's remove this file.

effigies · 2020-10-18T13:17:57Z

nibabel/imagestats.py

+import numpy as np
+
+
+def mask_volume(img, units='mm3'):


Thinking about this a bit, if units=="vox", then the output should be integer; there's no good reason to have a float for counting non-zero voxels. That makes the types a bit messy. What if we did (simplified):

def count_nonzero_voxels(img): return np.count_nonzero(img.dataobj) def mask_volume(img): nz_vox = count_nonzero_voxels(img) return np.prod(img.header.get_zooms()[:3]) * nz_vox

The conditional logic inside this function basically evaporates, and is moved into cmdline.stats.main to select which function to call.

Sounds good to me. I have simply left the code a bit more verbose for better readability.

Co-authored-by: Chris Markiewicz <[email protected]>

…eader.pixdim Co-authored-by: Chris Markiewicz <[email protected]>

…e in mm3 - use a mask-like volume for testing

effigies

Mostly style suggestions. And please use flake8 to check for any additional issues.

effigies · 2020-10-19T02:36:27Z

bin/nib-stats.py

+
+
+if __name__ == '__main__':
+    main()


Let's remove this file.

effigies · 2020-10-19T13:46:42Z

nibabel/cmdline/tests/test_stats.py

+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


Use the capsys fixture..

thanks, didn't know about that one

effigies · 2020-10-19T13:54:36Z

nibabel/funcs.py

@@ -215,3 +215,4 @@ 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)))
+


We don't need to touch this file.

nibabel/imagestats.py

nibabel/tests/test_imagestats.py

Co-authored-by: Chris Markiewicz <[email protected]>

JulianKlug · 2020-10-20T05:46:11Z

Sorry for the style issues. Should be fixed now.

effigies · 2020-10-20T11:58:21Z

Thanks a lot! This is a good start to a handy utility, and I look forward to seeing it grow.

Added a volume computation function

d7c7069

Compute volume of mask image. Equivalent to "fslstats /path/file.nii -V"

effigies mentioned this pull request Oct 16, 2020

REL: 3.2.0 #960

Merged

12 tasks

Added commandline and tests for imagestats volume computation

73bff0f

Fix style errors

57f7723

- blank lines - variable declaration in example

JulianKlug marked this pull request as ready for review October 18, 2020 07:43

effigies reviewed Oct 18, 2020

View reviewed changes

JulianKlug and others added 4 commits October 18, 2020 19:43

Apply suggestions from code review: Removing unused code

e15bb8d

Co-authored-by: Chris Markiewicz <[email protected]>

Apply suggestions from code review: Use header.get_zooms instead of h…

7412ba9

…eader.pixdim Co-authored-by: Chris Markiewicz <[email protected]>

Split Mask_volume into a function for voxels and a function for volum…

d357eae

…e in mm3 - use a mask-like volume for testing

Fix failing docstring

93532de

effigies reviewed Oct 19, 2020

View reviewed changes

JulianKlug and others added 2 commits October 19, 2020 22:10

Apply suggestions from code review

2331e9d

Co-authored-by: Chris Markiewicz <[email protected]>

Style issues, use capsys

35beaba

effigies merged commit 022832e into nipy:master Oct 20, 2020

Factral mentioned this pull request Feb 27, 2023

ENH: Make imagestats module available on import nibabel #1208

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NF: volume computation function for nifti masks #952

NF: volume computation function for nifti masks #952

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effigies commented Oct 20, 2020

		assert float(vol_mm3) == 2273328656.0
		assert float(vol_vox) == 284166082.0

	[options.entry_points]
	console_scripts =
	nib-conform=nibabel.cmdline.conform:main
	nib-ls=nibabel.cmdline.ls:main
	nib-dicomfs=nibabel.cmdline.dicomfs:main
	nib-diff=nibabel.cmdline.diff:main
	nib-nifti-dx=nibabel.cmdline.nifti_dx:main
	nib-tck2trk=nibabel.cmdline.tck2trk:main
	nib-trk2tck=nibabel.cmdline.trk2tck:main
	nib-roi=nibabel.cmdline.roi:main
	parrec2nii=nibabel.cmdline.parrec2nii:main

NF: volume computation function for nifti masks #952

NF: volume computation function for nifti masks #952

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