Source code for pyanno.plots.pyanno_plots

# Copyright (c) 2011, Enthought, Ltd.
# Author: Pietro Berkes <pberkes@enthought.com>
# License: Modified BSD license (2-clause)

from pyanno import measures
from pyanno.plots.matrix_plot import plot_square_matrix


def plot_pairwise_statistics(stat_func, annotations, nclasses=None, **kwargs):
    """Plot a matrix representation of a statistical function of annotations.

    The function `stat_func` is applied to the annotations of all pairs of
    annotators, and the resulting matrix is displayed in a window.

    Example: :::

       >>> plot_pairwise_statistics(pyanno.measures.cohens_kappa, annotations)

    See also :func:`pyanno.measures.helpers.pairwise_matrix`,
    :func:`~pyanno.plots.matrix_plot.plot_square_matrix`.

    Arguments
    ---------
    stat_func : function
        Function accepting as first two arguments two 1D array of
        annotations, and returning a single scalar measuring some annotations
        statistics.

    annotations : ndarray, shape = (n_items, n_annotators)
        Array of annotations for multiple annotators. Missing values should be
        indicated by :attr:`pyanno.util.MISSING_VALUE`

    nclasses : int
        Number of annotation classes. If None, `nclasses` is inferred from the
        values in the annotations

    kwargs : dictionary
        Additional keyword arguments passed to the plot. The argument 'title'
        sets the title of the plot.
    """

    if nclasses is None:
        measures.helpers.compute_nclasses(annotations)

    matrix = measures.pairwise_matrix(stat_func, annotations,
                                      nclasses=nclasses)

    kwargs_local = {'colormap_low': -1.0,
                    'colormap_high': 1.0}
    # add user kwargs, allowing for overwrite
    kwargs_local.update(kwargs)

    matrix_view = plot_square_matrix(matrix, **kwargs_local)
    return matrix_view



#### Testing and debugging ####################################################

def main():
    """ Entry point for standalone testing/debugging. """

    from pyanno.modelBt_loopdesign import ModelBtLoopDesign
    model = ModelBtLoopDesign.create_initial_state(4)
    annotations = model.generate_annotations(100)
    mv = plot_pairwise_statistics(measures.cohens_kappa, annotations)
    return mv


if __name__ == '__main__':
    mv = main()