# Resampling with scipy.ndimage

## Contents

# Resampling with `scipy.ndimage`

#

```
# import common modules
import numpy as np
np.set_printoptions(precision=4) # print arrays to 4DP
import matplotlib.pyplot as plt
plt.rcParams['image.cmap'] = 'gray'
```

## Reampling, pull, push#

Let us say we have two images \(\mathbf{I}\) and \(\mathbf{J}\).

There is some spatial transform between them, such as a translation, or rotation.

We could either think of the transformation that maps \(\mathbf{I} \to \mathbf{J}\) or \(\mathbf{J} \to \mathbf{I}\).

The transformations map voxel coordinates in one image to coordinates in the other.

For example, write a coordinate in \(\mathbf{I}\) as \((x_i, y_i, z_i)\), and a coordinate in \(\mathbf{J}\) as \((x_j, y_j, z_j)\).

The mapping \(\mathbf{I} \to \mathbf{J}\) maps \((x_i, y_i, z_i) \to (x_j, y_j, z_j)\).

Now let us say that we want to move image \(\mathbf{J}\) to match image \(\mathbf{I}\).

To do this moving, we need to resample \(\mathbf{J}\) onto the same voxel grid as \(\mathbf{I}\).

Specifically, we are going to do the following:

make a new empty image \(\mathbf{K}\) that has the same voxel grid as \(\mathbf{I}\);

for each coordinate in \(\mathbf{I} : (x_i, y_i, z_i)\) we will apply the transform \(\mathbf{I} \to \mathbf{J}\) to get \((x_j, y_j, z_j)\);

we will probably need to estimate a value \(v\) from \(\mathbf{J}\) at \((x_j, y_j, z_j)\) because the coordinate values \((x_j, y_j, z_j)\) will probably not be integers, and so there is no exactly matching value in \(\mathbf{J}\);

we place \(v\) into \(\mathbf{K}\) at coordinate \((x_i, y_i, z_i)\).

Notice that, in order to move \(\mathbf{J}\) to match \(\mathbf{I}\)
we needed the opposite transform – that is: \(\mathbf{I} \to
\mathbf{J}\). This is called *pull resampling*.

We will call the \(\mathbf{I} \to \mathbf{J}\) transform the *resampling
transform*.

## Scipy ndimage and affine_transform#

Scipy has a function for doing reampling with transformations, called scipy.ndimage.affine_transform.

```
from scipy.ndimage import affine_transform
```

It does all the heavy work of resampling for us.

For example, lets say we have an image volume \(\mathbf{I}\)
(`ds107_sub012_t1r2.nii`

):

```
# Fetch the data file.
import nipraxis
# Fetch image file.
bold_fname = nipraxis.fetch_file('ds107_sub012_t1r2.nii')
bold_fname
```

```
'/home/runner/.cache/nipraxis/0.5/ds107_sub012_t1r2.nii'
```

```
import nibabel as nib
img = nib.load(bold_fname)
data = img.get_fdata()
I = data[..., 0] # I is the first volume
```

We have another image volume \(\mathbf{J}\):

```
J = data[..., 1] # I is the second volume
```

Let’s say we know that the resampling transformation \(\mathbf{I} \to \mathbf{J}\) is given by:

a rotation by 0.2 radians about the x axis;

a translation of [1, 2, 3] voxels.

See Rotations and rotation matrices for more on 2D and 3D rotation matrices.

Here we use the nipraxis.rotations module. It has routines that will make 3 by 3 rotation matrices for rotations by given angles around the x, y, and z axes.

Of course you will want to be assured these functions are tested. Have a look at test_rotations.py.

We use the routines in the `nipraxis.rotations`

module to make the rotation
matrix we need:

```
from nipraxis.rotations import x_rotmat
# rotation matrix for rotation of 0.2 radians around x axis
M = x_rotmat(0.2)
M
translation = [1, 2, 3] # Translation from I to J
translation
```

```
[1, 2, 3]
```

The `affine_transform`

function does the work of resampling. By default, it
implements the following algorithm:

makes the new empty volume

`K`

, assuming it will be the same shape as`J`

;for each coordinate \((x_i, y_i, z_i)\) implied by the volume

`K`

:apply the transformations implied by

`M`

and`translation`

to \((x_i, y_i, z_i)\) to get the corresponding point in`J`

: \((x_j, y_j, z_j)\);resample

`J`

at \((x_j, y_j, z_j)\) to get \(v\);place \(v\) at \((x_i, y_i, z_i)\) in

`K`

```
# order=1 for linear interpolation
K = affine_transform(J, M, translation, order=1)
K.shape
plt.imshow(K[:, :, 17])
```

```
<matplotlib.image.AxesImage at 0x7fa672296790>
```

# Resampling with images of different shapes#

Notice the assumption that `affine_transform`

makes above – that the
output image will be the same shape as the input image.

This need not be the case. In fact we can tell `affine_transform`

to start
with an empty volume `K`

with another shape. To do this, we use the
`output_shape`

parameter.

Now we can be more precise about the algorithm of `affine_transform`

.
`affine_transform`

accepts:

`input`

– an array to resample from. Say this array as`n`

dimensions (`len(input.shape)`

);`matrix`

– an`n`

by`n`

transformation matrix (the top left`mat`

part of an affine);`offset`

– a optional length`n`

translation vector to be applied after the`matrix`

transformation (the`vec`

part of an affine);`output_shape`

: an optional tuple giving the shape of the output array into which we will put the values resampled from`input`

.`output_shape`

defaults to`input.shape`

; this is the default we have been using above.

`affine_transform`

then generates all the voxel coordinates *implied by* the
`output_shape`

, and transforms them with the `matrix`

and `offset`

transforms to get a new set of coordinates `C`

. It then samples the
`input`

array at the coordinates given by `C`

to generate the output
array.

Here is the call to `affine_transform`

that we used above, where we allowed
the routine to assume that the output shape was the same as the input shape:

```
K = affine_transform(J, M, translation, order=1)
K.shape
```

```
(64, 64, 35)
```

The is the same as the following call, where we specify the shape explicitly:

```
K = affine_transform(J, M, translation, output_shape=J.shape, order=1)
K.shape
```

```
(64, 64, 35)
```

The output shape can be different from the input shape:

```
K = affine_transform(J, M, translation,
output_shape=(65, 65, 36), order=1)
K.shape
```

```
(65, 65, 36)
```

Remember that the `M`

matrix and `translation`

vector apply to the
coordinates implied by the output shape.