This is a module for the Insight Toolkit (ITK) that provides functionality to discard pixels within a masked region. Unlike masking, the pixels in the masked region are replaced (dissolved) by their nearest pixels outside the mask. This can be useful to clean-up label fields, e.g. to remove small islands/holes or remove entire labels, and replace them by the adjacent labels.
The module includes a filter called DissolveMaskImageFilter.
import itk
labels = itk.imread('path/to/labels.mha').astype(itk.US)
mask = itk.imread('path/to/mask.mha').astype(itk.UC)
ImageType = type(labels)
MaskType = type(mask)
dissolve = itk.DissolveMaskImageFilter[ImageType, MaskType].New()
dissolve.SetInput(labels)
dissolve.SetMaskImage(mask)
dissolve.Update()
modified_labels = dissolve.GetOutput()
itk.imwrite(modified_labels, 'modified_labels2.mha')Or using the pythonic API:
import itk
labels = itk.imread('path/to/labels.mha').astype(itk.US)
mask = itk.imread('path/to/mask.mha').astype(itk.US)
modified_labels = itk.dissolve_mask_image_filter(labels, mask_image=mask)
itk.imwrite(modified_labels, 'path/to/modified_labels.mha')To install the binary Python packages:
python -m pip install itk-dissolve
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