nibabel_affines.Rmd

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# The [`nibabel.affines`](http://nipy.org/nibabel/reference/nibabel.affines.html#module-nibabel.affines) module

```{python}
import numpy as np
np.set_printoptions(precision=4, suppress=True)
import nibabel as nib
```

Neuroimaging images have affines, and we often need to process these
affines, or apply these affines to coordinates.

Nibabel has routines to do this in its `affines` submodule.

The `from_matvec` function is a short-cut to make a 4 x 4 affine matrix from
a 3 x 3 matrix and an (optional) vector of translations.

For example, let’s say I have a 3 x 3 rotation matrix, specifying a rotation
of 0.4 radians around the y axis (see Rotations and rotation matrices):

```{python}
cos_a = np.cos(0.4)
sin_a = np.sin(0.4)
y_rotation = np.array([[ cos_a,    0,  sin_a],
                       [     0,    1,      0],
                       [-sin_a,    0,  cos_a]])
y_rotation
```

I want to put this 3 x 3 matrix into a 4 x 4 affine matrix:

```{python}
# Affine from a 3x3 matrix (the 'mat' in 'matvec')
nib.affines.from_matvec(y_rotation)
```

You can also add a translation vector in the call to `from_matvec`.  The
translation vector is the `vec` of `from_matvec`:

```{python}
# Affine from a 3x3 matrix ('mat') and a translation vector ('vec')
aff = nib.affines.from_matvec(y_rotation, [10, 20, 30])
aff
```

`nibabel.affines.to_matvec` does the reverse operation.  It splits the
affine matrix into the top left 3 x 3 matrix, and the translation vector from
the last column of the affine:

```{python}
mat, vec = nib.affines.to_matvec(aff)
mat
vec
```