Clarification to docs regarding initial sform/qform code values #576
Conversation
…ecified during Nifti1Image creation.
…ow the sform/qform codes are initialised.
nibabel/nifti1.py
Outdated
| ``affine`` does not match the affine that is in the ``header``, | ||
| the ``affine`` will be used, but the ``sform_code`` and | ||
| ``qform_code`` fields in the header will be re-initialised to | ||
| their default values.. This is performed on the basis that, if |
Codecov Report
@@ Coverage Diff @@
## master #576 +/- ##
=======================================
Coverage 94.32% 94.32%
=======================================
Files 177 177
Lines 24695 24695
Branches 2639 2639
=======================================
Hits 23294 23294
Misses 925 925
Partials 476 476
Continue to review full report at Codecov.
|
doc/source/nifti_images.rst
Outdated
| The sform and qform codes will be initialised to 2 (aligned) and 0 (unknown) | ||
| respectively: | ||
|
|
||
| >>> img.get_sform(coded=True) |
There was a problem hiding this comment.
>>> img.get_sform(coded=True) # doctest: +NORMALIZE_WHITESPACE
|
Oops. You got to the typo before me. |
doc/source/nifti_images.rst
Outdated
| >>> new_data = np.random.random(n1_img.shape[:3]) | ||
| >>> new_img = nib.nifti1.Nifti1Image(data, None, header=new_header) | ||
|
|
||
| Then the newly created image will inherit the same sform and qform codes that |
There was a problem hiding this comment.
Capital T for Then reads oddly.
nibabel/nifti1.py
Outdated
| Notes | ||
| ----- | ||
|
|
||
| If both a ``header`` and an ``affine`` are specified, and the ``affine`` |
There was a problem hiding this comment.
I think you want single backticks for the parameters header and affine.
There was a problem hiding this comment.
I think it's a single backtick for markdown, but double backticks for restructured text - this renders fine as it is.
There was a problem hiding this comment.
Single backticks in rst gives the default markup, which, in the case of the numpy docstring renderer, has the right markup for referring to parameters. So, single backticks to refer to parameters, double backticks for typewriter font ...
There was a problem hiding this comment.
Aah ok - I am not all that familiar with numpydoc - will fix it now!
|
Great - thanks for your patience. |
[see #574 for background]
This PR adds a little bit of documentation to the
Nifti1Pairclass, and to the nibabel user documentation page on working with NIfTI images, clarifying how thesform_codeandqform_codefields are initialised under different circumstances.