def single_envelope(outcomes,
outcome_to_plot,
time,
density,
ax,
ax_d,
fill,
**kwargs):
'''
Helper function for generating a single envelope plot.
:param outcomes: a dictonary containing the various outcomes to plot
:param outcome_to_plot: the specific outcome to plot
:param time: the name of the time dimension
:param density: string, either hist, kde, or empty/None.
:param ax: the ax on which to plot
:param ax_d: the ax on which to plot the density
:param fill: boolean, if true, fill the envelope.
:param kwargs: kwargs to be passed on to the hlepr function for plotting
the density.
'''
value = outcomes[outcome_to_plot]
plot_envelope(ax, 0, time, value,fill)
if density:
simple_density(density, value, ax_d, ax, **kwargs)
def group_by_envelopes(outcomes,
outcome_to_plot,
time,
density,
ax,
ax_d,
fill,
group_labels,
**kwargs):
'''
Helper function, responsible for generating an envelope plot based on
a grouping.
:param outcomes: a dictonary containing the various outcomes to plot
:param outcome_to_plot: the specific outcome to plot
:param time: the name of the time dimension
:param density: string, either hist, kde, or empty/None.
:param ax: the ax on which to plot
:param ax_d: the ax on which to plot the density
:param fill: boolean, if true, fill the envelope.
:param group_by_labels: order in which groups should be plotted
:param kwargs: kwargs to be passed on to the helper function for plotting
the density.
'''
for j, key in enumerate(group_labels):
value = outcomes[key]
value = value[outcome_to_plot]
try:
plot_envelope(ax, j, time, value,fill)
except ValueError:
warning("value error when plotting for %s" % (key))
raise
if density=='kde':
kde_x, kde_y = determine_kde(value[:,-1])
plot_kde(ax_d, kde_x, kde_y, j, **kwargs)
if density:
if density=='hist':
# rather nasty indexing going on here, outcomes[key] returns
# a tuple, hence the[1] to get the dictonary with outcomes
# out of this, we need the right outcome, and the final column
# of values
values = [outcomes[key][outcome_to_plot][:,-1] for key in group_labels]
plot_histogram(ax_d, values, **kwargs)
if density=='box plot':
values = [outcomes[key][outcome_to_plot][:,-1] for key in group_labels]
plot_boxplots(ax_d, values, group_labels, **kwargs)
ax_d.get_yaxis().set_view_interval(
ax.get_yaxis().get_view_interval()[0],
ax.get_yaxis().get_view_interval()[1])
def group_by_envelopes(outcomes,
outcome_to_plot,
time,
density,
ax,
ax_d,
fill,
group_labels,
log):
'''
Helper function, responsible for generating an envelope plot based on
a grouping.
:param outcomes: a dictonary containing the various outcomes to plot
:param outcome_to_plot: the specific outcome to plot
:param time: the name of the time dimension
:param density: string, either hist, kde, or empty/None.
:param ax: the ax on which to plot
:param ax_d: the ax on which to plot the density
:param fill: boolean, if true, fill the envelope.
:param group_by_labels: order in which groups should be plotted
:param log: boolean, log scale density plot
'''
for j, key in enumerate(group_labels):
value = outcomes[key]
value = value[outcome_to_plot]
try:
plot_envelope(ax, j, time, value,fill)
except ValueError:
warning("value error when plotting for %s" % (key))
raise
if density:
group_density(ax_d, density, outcomes, outcome_to_plot, group_labels,
log)
ax_d.get_yaxis().set_view_interval(
ax.get_yaxis().get_view_interval()[0],
ax.get_yaxis().get_view_interval()[1])
def multiple_densities(results,
outcomes_to_show=[],
points_in_time=[],
group_by = None,
grouping_specifiers = None,
density=KDE,
titles={},
ylabels={},
legend=True,
experiments_to_show=None,
plot_type = ENVELOPE,
**kwargs):
'''
Make an envelope plot with multiple density plots over the run time
:param results: return from :meth:`perform_experiments`.
:param outcomes_to_show: list of outcome of interest you want to plot. If
empty, all outcomes are plotted. **Note**: just
names.
:param points_in_time: a list of points in time for which you want to see
the density. At the moment up to 6 points in time
are supported.
:param group_by: name of the column in the cases array to group results by.
Alternatively, `index` can be used to use indexing arrays
as the basis for grouping.
:param grouping_specifiers: set of categories to be used as a basis for
grouping by. Grouping_specifiers is only
meaningful if group_by is provided as well. In
case of grouping by index, the grouping
specifiers should be in a dictonary where the
key denotes the name of the group.
:param density: field, either KDE or HIST
:param titles: a way for controlling whether each of the axes should have
a title. There are three possibilities. If set to None, no
title will be shown for any of the axes. If set to an empty
dict, the default, the title is identical to the name of the
outcome of interest. If you want to override these default
names, provide a dict with the outcome of interest as key
and the desired title as value. This dict need only contain
the outcomes for which you want to use a different title.
:param ylabels: a way for controlling the ylablels. Works identical to
titles.
:param legend: boolean, if true, and there is a column specified for
grouping, show a legend.
:param experiments_to_show: numpy array containing the indices of the
experiments to be visualized. Defaults to None,
implying that all experiments should be shown.
:plot_type: kwarg for controling the type of main plot. Can be one of
ENVELOPE, LINES, or ENV_LIN
:rtype: a `figure <http://matplotlib.sourceforge.net/api/figure_api.html>`_ instance
Additional key word arguments will be passed along to the density function,
======== ===================================
property description
======== ===================================
log log the resulting histogram or GKDE
======== ===================================
.. rubric:: an example of use
.. note:: the current implementation is limited to seven different
categories in case of column, categories, and/or discretesize.
This limit is due to the colors specified in COLOR_LIST.
.. note:: the connection patches are for some reason not drawn if log
scaling is used for the density plots. This appears to be an
issue in matplotlib itself.
'''
if not outcomes_to_show:
outcomes_to_show = results[1].keys()
outcomes_to_show.remove(TIME)
elif type(outcomes_to_show)==StringType:
outcomes_to_show=[outcomes_to_show]
axes_dicts = {}
for outcome_to_show in outcomes_to_show:
axes_dict = {}
axes_dicts[outcome_to_show] = axes_dict
if plot_type != ENV_LIN:
# standard way of pre processing data
if experiments_to_show != None:
experiments, outcomes = results
experiments = experiments[experiments_to_show]
new_outcomes = {}
for key, value in outcomes.items():
new_outcomes[key] = value[experiments_to_show]
results = experiments, new_outcomes
data = prepare_data(results, [outcome_to_show], group_by,
grouping_specifiers)
outcomes, outcomes_to_show, time, grouping_labels = data
del outcomes_to_show
#start of plotting
fig = plt.figure()
axes_dict["fig"] = fig
# making of grid
if not points_in_time:
raise EMAError("no points in time specified")
if len(points_in_time) == 1:
ax_env = plt.subplot2grid((2,3), (0,0), colspan=3)
ax1 = plt.subplot2grid((2,3), (1,1), )
kde_axes = [ax1]
elif len(points_in_time) == 2:
ax_env = plt.subplot2grid((2,2), (0,0), colspan=2)
ax1 = plt.subplot2grid((2,2), (1,0), )
ax2 = plt.subplot2grid((2,2), (1,1), sharex=ax1)
kde_axes = [ax1, ax2]
elif len(points_in_time) == 3:
ax_env = plt.subplot2grid((2,3), (0,0), colspan=3)
ax1 = plt.subplot2grid((2,3), (1,0), )
ax2 = plt.subplot2grid((2,3), (1,1), sharex=ax1)
ax3 = plt.subplot2grid((2,3), (1,2), sharex=ax1)
kde_axes = [ax1, ax2, ax3]
elif len(points_in_time) == 4:
ax_env = plt.subplot2grid((2,4), (0,1), colspan=2)
ax1 = plt.subplot2grid((2,4), (1,0), )
ax2 = plt.subplot2grid((2,4), (1,1), sharex=ax1)
ax3 = plt.subplot2grid((2,4), (1,2), sharex=ax1)
ax4 = plt.subplot2grid((2,4), (1,3), sharex=ax1)
kde_axes = [ax1, ax2, ax3, ax4]
elif len(points_in_time) == 5:
ax_env = plt.subplot2grid((2,5), (0,1), colspan=3)
ax1 = plt.subplot2grid((2,5), (1,0), )
ax2 = plt.subplot2grid((2,5), (1,1), sharex=ax1)
ax3 = plt.subplot2grid((2,5), (1,2), sharex=ax1)
ax4 = plt.subplot2grid((2,5), (1,3), sharex=ax1)
ax5 = plt.subplot2grid((2,5), (1,4), sharex=ax1)
kde_axes = [ax1, ax2, ax3, ax4, ax5]
elif len(points_in_time) == 6:
ax_env = plt.subplot2grid((2,6), (0,1), colspan=4)
ax1 = plt.subplot2grid((2,6), (1,0), )
ax2 = plt.subplot2grid((2,6), (1,1), sharex=ax1)
ax3 = plt.subplot2grid((2,6), (1,2), sharex=ax1)
ax4 = plt.subplot2grid((2,6), (1,3), sharex=ax1)
ax5 = plt.subplot2grid((2,6), (1,4), sharex=ax1)
ax6 = plt.subplot2grid((2,6), (1,5), sharex=ax1)
kde_axes = [ax1, ax2, ax3, ax4, ax5, ax6, ]
else:
raise EMAError("too many points in time provided")
axes_dict["main plot"] = ax_env
for n, entry in enumerate(kde_axes):
axes_dict["density_%s" % n] = entry
#turn of ticks for all but the first density
if n > 0:
for tl in entry.get_yticklabels():
tl.set_visible(False)
# bit of a trick to avoid duplicating code. If no subgroups are
# specified, nest the outcomes one step deeper in de dict so the
# iteration below can proceed normally.
if not grouping_labels:
grouping_labels=[""]
outcomes[""]=outcomes
max_x = 0
for j, key in enumerate(grouping_labels):
value = outcomes[key][outcome_to_show]
if plot_type == ENVELOPE:
plot_envelope(ax_env, j, time, value, fill=False)
elif plot_type == LINES:
ax_env.plot(time.T, value.T)
elif plot_type == ENV_LIN:
plot_envelope(ax_env, j, time, value, fill=True)
if experiments_to_show!=None:
ax_env.plot(time.T, value[experiments_to_show].T)
else:
ax_env.plot(time.T, value.T)
ax_env.set_xlim(time[0], time[-1])
ax_env.set_xlabel(TIME_LABEL)
do_ylabels(ax_env, ylabels, outcome_to_show)
do_titles(ax_env, titles, outcome_to_show)
# this might seem a bit strange but under some conditions can the
# autoscaling of the y_axis be # changed due to the plot command
# for the crossection line. This overrides the autoscaling
# updating.
min_y, max_y = ax_env.get_ylim()
ax_env.autoscale(enable=False, axis='y')
for i, ax in enumerate(kde_axes):
time_value = points_in_time[i]
if time_value:
index = np.where(time==points_in_time[i])[0][0]
if density==KDE:
kde_x, kde_y = determine_kde(value[:,index])
plot_kde(ax, kde_x, kde_y, j,**kwargs)
#update max_x
max_kde =np.max(kde_x)
if max_kde > max_x and max_kde < 10:
max_x = max_kde
ax_env.plot([points_in_time[i],points_in_time[i]],
[min_y,max_y], c='k', ls='--')
con = ConnectionPatch(xyA=(time_value, 0),
xyB=(min_y,max_y), coordsA="data",
coordsB="data", axesA=ax_env,
axesB=ax)
ax_env.add_artist(con)
if density == HIST:
for i, ax in enumerate(kde_axes):
time_value = points_in_time[i]
index = np.where(time==points_in_time[i])[0][0]
values = [outcomes[key][outcome_to_show][:,index] for key in\
grouping_labels]
n, bins, patches = plot_histogram(ax, values, **kwargs)
del bins, patches
if np.max(n) > max_x and np.max(n)<10:
max_x = np.max(n)
for ax in kde_axes:
ax.get_yaxis().set_view_interval(
ax_env.get_yaxis().get_view_interval()[0],
ax_env.get_yaxis().get_view_interval()[1])
# ax.set_xlim(xmin=0,xmax=math.ceil(max_x))
ax.set_xlim(xmin=0,xmax=max_x)
if legend and group_by:
make_legend(grouping_labels, fig)
return fig, axes_dicts
def plot_lines_with_envelopes(results,
outcomes_to_show = [],
group_by = None,
grouping_specifiers = None,
density='',
titles={},
ylabels={},
legend=True,
experiments_to_show=None,
**kwargs):
'''
Helper function for generating a plot which contains both an envelope and
lines.
:param results: return from :meth:`perform_experiments`.
:param outcomes_to_show: list of outcome of interest you want to plot. If
empty, all outcomes are plotted. **Note**: just
:param group_by: name of the column in the cases array to group results by.
Alternatively, `index` can be used to use indexing arrays
as the basis for grouping.
:param grouping_specifiers: set of categories to be used as a basis for
grouping by. Grouping_specifiers is only
meaningful if group_by is provided as well. In
case of grouping by index, the grouping
specifiers should be in a dictonary where the
key denotes the name of the group.
:param density: boolean, if true, the density of the endstates will be
plotted.
:param titles: a way for controlling whether each of the axes should have
a title. There are three possibilities. If set to None, no
title will be shown for any of the axes. If set to an empty
dict, the default, the title is identical to the name of the
outcome of interest. If you want to override these default
names, provide a dict with the outcome of interest as key
and the desired title as value. This dict need only contain
the outcomes for which you want to use a different title.
:param ylabels: a way for controlling the ylablels. Works identical to
titles.
:param legend: boolean, if true, and there is a column specified for
grouping, show a legend
:param experiments_to_show: numpy array containing the indices of the
experiments to be visualized. Defaults to None,
implying that all experiments should be shown.
:rtype: a `figure <http://matplotlib.sourceforge.net/api/figure_api.html>`_ instance
Additional key word arguments will be passed along to the density function.
======== ===============================
property description
======== ===============================
log log scale the histogram or GKDE
======== ===============================
'''
# make sure we have the data
full_results = copy.deepcopy(results)
experiments, outcomes = results
experiments = experiments[experiments_to_show]
new_outcomes={}
for key, value in outcomes.items():
new_outcomes[key] =value[experiments_to_show]
results = experiments, new_outcomes
data = prepare_data(results, outcomes_to_show, group_by,
grouping_specifiers)
outcomes, outcomes_to_show, time, grouping_labels = data
full_outcomes = prepare_data(full_results, outcomes_to_show, group_by,
grouping_specifiers)[0]
figure, grid = make_grid(outcomes_to_show, density)
axes_dict = {}
# do the plotting
for i, outcome_to_plot in enumerate(outcomes_to_show):
ax = figure.add_subplot(grid[i,0])
axes_dict[outcome_to_plot] = ax
ax_d= None
if density:
ax_d = figure.add_subplot(grid[i,1])
axes_dict[outcome_to_plot+"_density"] = ax_d
for tl in ax_d.get_yticklabels():
tl.set_visible(False)
if group_by:
# group_by_labels = sorted(outcomes.keys())
for j, key in enumerate(grouping_labels):
full_value = full_outcomes[key][outcome_to_plot]
plot_envelope(ax, j, time, full_value, fill=True)
for j, key in enumerate(grouping_labels):
value = outcomes[key][outcome_to_plot]
full_value = full_outcomes[key][outcome_to_plot]
ax.plot(time.T[:, np.newaxis], value.T, COLOR_LIST[j])
if density=='kde':
simple_density(density, full_value, ax_d, ax, **kwargs)
# kde_x, kde_y = determine_kde(full_value[:,-1])
# plot_kde(ax_d, kde_x, kde_y, j, **kwargs)
if density:
if density=='hist':
values = [full_outcomes[key][outcome_to_plot][:,-1]\
for key in grouping_labels]
plot_histogram(ax_d, values, **kwargs)
ax_d.get_yaxis().set_view_interval(
ax.get_yaxis().get_view_interval()[0],
ax.get_yaxis().get_view_interval()[1])
else:
value = full_outcomes[outcome_to_plot]
plot_envelope(ax, 0, time, value, fill=True)
if density:
simple_density(density, value, ax_d, ax, **kwargs)
value = outcomes[outcome_to_plot]
ax.plot(time.T, value.T)
ax.set_xlim(xmin=time[0] , xmax=time[-1])
ax.set_xlabel(TIME_LABEL)
do_ylabels(ax, ylabels, outcome_to_plot)
do_titles(ax, titles, outcome_to_plot)
if legend and group_by:
make_legend(grouping_labels, figure)
if plotting_util.TIGHT:
grid.tight_layout(figure)
return figure, axes_dict