skimage2.segmentation.morphological_geodesic_active_contour

skimage2.segmentation.morphological_geodesic_active_contour(gimage, num_iter, init_level_set='disk', smoothing=1, threshold='auto', balloon=0, iter_callback=<function <lambda>>)

Morphological Geodesic Active Contours (MorphGAC).

Geodesic active contours implemented with morphological operators. It can be used to segment objects with visible but noisy, cluttered, broken borders.

Parameters:

gimage(M, N) or (L, M, N) array

Preprocessed image or volume to be segmented. This is very rarely the original image. Instead, this is usually a preprocessed version of the original image that enhances and highlights the borders (or other structures) of the object to segment. morphological_geodesic_active_contour() will try to stop the contour evolution in areas where gimage is small. See inverse_gaussian_gradient() as an example function to perform this preprocessing. Note that the quality of morphological_geodesic_active_contour() might greatly depend on this preprocessing.

num_iteruint

Number of num_iter to run.

init_level_setstr, (M, N) array, or (L, M, N) array

Initial level set. If an array is given, it will be binarized and used as the initial level set. If a string is given, it defines the method to generate a reasonable initial level set with the shape of the image. Accepted values are ‘checkerboard’ and ‘disk’. See the documentation of checkerboard_level_set and disk_level_set respectively for details about how these level sets are created.

smoothinguint, optional

Number of times the smoothing operator is applied per iteration. Reasonable values are around 1-4. Larger values lead to smoother segmentations.

thresholdfloat, optional

Areas of the image with a value smaller than this threshold will be considered borders. The evolution of the contour will stop in these areas.

balloonfloat, optional

Balloon force to guide the contour in non-informative areas of the image, i.e., areas where the gradient of the image is too small to push the contour towards a border. A negative value will shrink the contour, while a positive value will expand the contour in these areas. Setting this to zero will disable the balloon force.

iter_callbackfunction, optional

If given, this function is called once per iteration with the current level set as the only argument. This is useful for debugging or for plotting intermediate results during the evolution.

Returns:

out(M, N) or (L, M, N) array

Final segmentation (i.e., the final level set)

See also

inverse_gaussian_gradient, disk_level_set, checkerboard_level_set

Notes

This is a version of the Geodesic Active Contours (GAC) algorithm that uses morphological operators instead of solving partial differential equations (PDEs) for the evolution of the contour. The set of morphological operators used in this algorithm are proved to be infinitesimally equivalent to the GAC PDEs (see [1]). However, morphological operators are do not suffer from the numerical stability issues typically found in PDEs (e.g., it is not necessary to find the right time step for the evolution), and are computationally faster.

The algorithm and its theoretical derivation are described in [1].

References

[1] (1,2)

A Morphological Approach to Curvature-based Evolution of Curves and Surfaces, Pablo Márquez-Neila, Luis Baumela, Luis Álvarez. In IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), 2014, DOI:10.1109/TPAMI.2013.106