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GASP

Generalized Algorithm for Signed graph Partitioning

Installation

  • On Linux and Mac, the package can be easily installed via conda:
    • conda create -n GASP -c conda-forge -c abailoni gasp
    • Activate your new environment: conda activate GASP

How to use the package

Examples

In the folder examples there are some scripts to run the GASP algorithm directly on a graph or on affinities generated from an image.

Running GASP on a graph

The main function to run GASP on a graph (that can be built using the nifty package) is given by from GASP.segmentation import run_GASP:

run_GASP(
        graph,
        signed_edge_weights,
        linkage_criteria='mean',
        add_cannot_link_constraints=False,
        edge_sizes=None,
        is_mergeable_edge=None,
        use_efficient_implementations=True,
        verbose=False,
        linkage_criteria_kwargs=None,
        print_every=100000)

with the following parameters:

  • graph :

    Instance of a nifty.graph, e.g. nifty.graph.UndirectedGraph, nifty.graph.undirectedLongRangeGridGraph or nifty.graph.rag.gridRag

  • signed_edge_weights : numpy.array(float)

    Array with shape (nb_graph_edges, ). Attractive weights are positive; repulsive weights are negative.

  • linkage_criteria : str (default mean)

    Specifies the linkage criteria / update rule used during agglomeration

    • mean, average, avg
    • max, single_linkage
    • min, complete_linkage
    • mutex_watershed, abs_max
    • sum
    • quantile, rank keeps statistics in a histogram, with parameters:
      • q : float (default 0.5 equivalent to the median)
      • numberOfBins: int (default: 40)
    • generalized_mean, gmean (https://en.wikipedia.org/wiki/Generalized_mean) with parameters:
      • p : float (default: 1.0)
    • smooth_max, smax (https://en.wikipedia.org/wiki/Smooth_maximum) with parameters:
      • p : float (default: 0.0)

  • add_cannot_link_constraints : bool

  • edge_sizes : numpy.array(float) with shape (nb_graph_edges, )

    Depending on the linkage criteria, they can be used during the agglomeration to weight differently the edges (e.g. with sum or avg linkage criteria). Commonly used with regionAdjGraphs when edges represent boundaries of different length between segments / super-pixels. By default, all edges have the same weighting.

  • is_mergeable_edge : numpy.array(bool) with shape (nb_graph_edges, )

    Specifies if an edge can be merged or not. Sometimes some edges represent direct-neighbor relations and others describe long-range connections. If a long-range connection /edge is assigned to is_mergeable_edge = False, then the two associated nodes are not merged until they become direct neighbors and they get connected in the image-plane. By default all edges are mergeable.

  • use_efficient_implementations : bool (default: True)

    In the following special cases, alternative efficient implementations are used:

  • verbose : bool (default: False)

  • linkage_criteria_kwargs : dict

    Additional optional parameters passed to the chosen linkage criteria (see previous list)

  • print_every : int (default: 100000)

    After how many agglomeration iteration to print in verbose mode

Image segmentation with GASP

For more details about it, see example examples/run_GASP_from_affinities.py and the docstrings of the class GASP.segmentation.GaspFromAffinities:

class GaspFromAffinities(object):
    def __init__(self,
                 offsets,
                 beta_bias=0.5,
                 superpixel_generator=None,
                 run_GASP_kwargs=None,
                 n_threads=1,
                 verbose=False,
                 invert_affinities=False,
                 offsets_probabilities=None,
                 use_logarithmic_weights=False,
                 used_offsets=None,
                 offsets_weights=None):
        ...

     def __call__(self, affinities, *args_superpixel_gen):
        ...