Repeated DenseFieldTransform.map calls are unnecessarily slow

[chriscline]

For each call to scipy.ndimage.map_coordinates (here) , a spline filter is re-applied to the field (here). This adds substantial time to repeated mapping calls on the same field.

If we can apply the spline filter once and save the results, we can then provide the filtered field directly to map_coordinates and specify prefilter=False to avoid re-applying the filter.

[chriscline]

With the proposed changes, the following example code demonstrates the speedup of pre-filtering:

import timeit
import numpy as np
import nibabel as nib
import nitransforms as nit

transformFilepath ='example.nii.gz'

field = nib.load(transformFilepath)

def create_transform(do_prefilter: bool):
    return nit.nonlinear.DenseFieldTransform(
        field=field,
        is_deltas=False,
        do_prefilter=do_prefilter
    )

transf_prefiltered = create_transform(do_prefilter=True)

transf_notfiltered = create_transform(do_prefilter=False)

inputCoords = np.random.rand(10, 3)

outputCoords_prefiltered = transf_prefiltered.map(inputCoords)
outputCoords_notfiltered = transf_notfiltered.map(inputCoords)

assert np.allclose(outputCoords_prefiltered, outputCoords_notfiltered), "Outputs do not match!"

def map(transform: nit.nonlinear.DenseFieldTransform):
    out_coords = transform.map(inputCoords)
    return out_coords

numRepeats = 10

duration = timeit.timeit(lambda: create_transform(do_prefilter=True), number=numRepeats)
print(f'Average time per creation for prefiltered: {duration / numRepeats:.6f} seconds')

duration = timeit.timeit(lambda: create_transform(do_prefilter=False), number=numRepeats)
print(f'Average time per creation for not prefiltered: {duration / numRepeats:.6f} seconds')

duration = timeit.timeit(lambda: map(transf_prefiltered), number=numRepeats)
print(f'Average time per map for prefiltered: {duration / numRepeats:.6f} seconds')

duration = timeit.timeit(lambda: map(transf_notfiltered), number=numRepeats)
print(f'Average time per map for not prefiltered: {duration / numRepeats:.6f} seconds')

From which the output is

Average time per creation for prefiltered: 2.826246 seconds
Average time per creation for not prefiltered: 1.899202 seconds
Average time per map for prefiltered: 0.000050 seconds
Average time per map for not prefiltered: 0.557268 seconds