How to use the pypesto.visualize.clust_color.assign_colors function in pypesto

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github ICB-DCM / pyPESTO / pypesto / visualize / parameters.py View on Github external
xs = np.array(xs)
    fvals = np.array(fvals)
    # remove nan or inf values in fvals and xs
    xs, fvals = delete_nan_inf(fvals, xs)

    if size is None:
        # 0.5 inch height per parameter
        size = (18.5, max(xs.shape[1], 1) / 2)

    if ax is None:
        ax = plt.subplots()[1]
        fig = plt.gcf()
        fig.set_size_inches(*size)

    # assign colors
    colors = assign_colors(vals=fvals, colors=colors,
                           balance_alpha=balance_alpha)

    # parameter indices
    parameters_ind = list(range(1, xs.shape[1] + 1))[::-1]

    # plot parameters
    ax.xaxis.set_major_locator(MaxNLocator(integer=True))
    for j_x, x in reversed(list(enumerate(xs))):
        if j_x == 0:
            tmp_legend = legend_text
        else:
            tmp_legend = None
        ax.plot(x, parameters_ind,
                linestyle,
                color=colors[j_x],
                marker='o',
github ICB-DCM / pyPESTO / pypesto / visualize / profiles.py View on Github external
legend_text: str
        Label for line plots

    Returns
    -------

    ax: matplotlib.Axes
        The plot axes.
    """

    # parse input
    fvals = np.array(fvals)

    # get colors
    color = assign_colors([1.], color)

    # axes
    if ax is None:
        ax = plt.subplots()[1]
        ax.set_xlabel('Parameter value')
        ax.set_ylabel('Log-posterior ratio')
        fig = plt.gcf()
        fig.set_size_inches(*size)

    # plot
    if fvals.size != 0:
        ax.xaxis.set_major_locator(MaxNLocator(integer=True))
        ax.plot(fvals[0, :], fvals[1, :], color=color[0], label=legend_text)

    if legend_text is not None:
        ax.legend()
github ICB-DCM / pyPESTO / pypesto / visualize / misc.py View on Github external
# check how many results were passed
    single_result = False
    legend_error = False
    if isinstance(results, list):
        if len(results) == 1:
            single_result = True
    else:
        single_result = True
        results = [results]

    # handle results according to their number
    if single_result:
        # assign colors and create list for later handling
        if colors is not None:
            colors = assign_colors(results, colors)
        colors = [colors]

        # create list of legends for later handling
        if not isinstance(legends, list):
            legends = [legends]
    else:
        # if more than one result is passed, we use one color per result
        colors = assign_colors_for_result_list(len(results), colors)

        # check whether list of legends has the correct length
        if legends is None:
            # No legends were passed: create some custom legends
            legends = []
            for i_leg in range(len(results)):
                legends.append('Result ' + str(i_leg))
        else:
github ICB-DCM / pyPESTO / pypesto / visualize / optimization_stats.py View on Github external
The plot axes.
    """

    fvals = result.optimize_result.get_for_key('fval')
    values = result.optimize_result.get_for_key(key)
    values, fvals = delete_nan_inf(fvals, values)

    if start_indices is not None:
        start_indices = process_start_indices(start_indices, len(values))
        values = values[start_indices]
        fvals = fvals[start_indices]

    n_starts = len(values)

    # assign colors
    colors = assign_colors(vals=fvals, colors=color,
                           balance_alpha=False)

    # sort TODO: issue # 378
    sorted_indices = sorted(range(n_starts), key=lambda j: fvals[j])
    values = values[sorted_indices]

    if plot_type == 'line':
        # plot line
        ax.plot(range(n_starts), values, color=[0.7, 0.7, 0.7, 0.6])

        # plot points
        for i, v in enumerate(values):
            if i == 0:
                tmp_legend = legend
            else:
                tmp_legend = None
github ICB-DCM / pyPESTO / pypesto / visualize / optimizer_history.py View on Github external
val = np.array(val)
            fvals.append(val[1, -1])
    else:
        # convert to a list of numpy arrays
        vals = np.array(vals)
        if vals.shape[0] != 2 or vals.ndim != 2:
            raise ('If numpy array is passed directly to lowlevel routine of'
                   'optimizer_history, shape needs to be 2 x n.')
        fvals = [vals[1, -1]]
        vals = [vals]
    n_fvals = len(fvals)

    # assign colors
    # note: this has to happen before sorting
    # to get the same colors in different plots
    colors = assign_colors(fvals, colors)

    # sort
    indices = sorted(range(n_fvals), key=lambda j: fvals[j])

    # plot
    ax.xaxis.set_major_locator(MaxNLocator(integer=True))
    for j, val in enumerate(vals):
        # collect and parse data
        j_fval = indices[j]
        color = colors[j_fval]
        if j == 0:
            tmp_legend = legend_text
        else:
            tmp_legend = None

        # line plots