Python examples

[simeks]

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[simeks]

Basic example:

import pydeform

settings = {
    'step_size': 0.2
}

fixed = pydeform.read_volume('fixed.nrrd')
moving = pydeform.read_volume('moving.nrrd')

df = pydeform.register(fixed, moving, settings = settings)

pydeform.write_volume('result.nrrd', df)

Image API:

import pydeform

# Read a volume
volume = pydeform.read_volume('image.nrrd')

# Creates a copy of the image data
array1 = np.array(volume)

# Reference to image data, enabling editing of 'img' object
array2 = np.array(volume, copy=False)
array2[0,0,0] = 1

# Create a new Volume object, for input to registration:
new_volume = pydeform.Volume(
    array1,
    origin = volume.origin,
    spacing = volume.spacing
)

# ...
pydeform.register(volume, new_volume)

Regularization weight map:

import pydeform

settings = {
    'step_size': 0.2
}

fixed = pydeform.read_volume('fixed.nrrd')
moving = pydeform.read_volume('moving.nrrd')

# Retrieve fixed image data
fixed_data = np.array(fixed)

# Create a regularization map
regmap = pydeform.Volume(
    (fixed_data > 0.5)*0.5, # Only regularize voxels with intensities larger than 0.5
)

# Don't forget meta data
regmap.copy_meta_from(fixed)

# Perform registration
df = pydeform.register(
    fixed,
    moving,
    regularization_map = regmap,
    settings = settings
)

pydeform.write_volume('result.nrrd', df)