class BoxPlotPanel(FigureCanvasWxAgg):
def __init__(self, parent, points, **kwargs):
'''
points -- a dictionary mapping x axis values to lists of values to plot
'''
self.figure = Figure()
FigureCanvasWxAgg.__init__(self, parent, -1, self.figure, **kwargs)
self.canvas = self.figure.canvas
self.SetMinSize((100,100))
self.figure.set_facecolor((1,1,1))
self.figure.set_edgecolor((1,1,1))
self.canvas.SetBackgroundColour('white')
self.navtoolbar = None
self.setpoints(points)
def setpoints(self, points):
'''
Updates the data to be plotted and redraws the plot.
points - list of array samples, where each sample will be plotted as a
separate box plot against the same y axis
'''
self.xlabels = []
self.points = []
ignored = 0
for label, values in sorted(points.items()):
if type(label) in [tuple, list]:
self.xlabels += [','.join([str(l) for l in label])]
else:
self.xlabels += [label]
self.points += [np.array(values).astype('f')[~ np.isnan(values)]]
ignored += len(np.array(values)[np.isnan(values)])
if not hasattr(self, 'subplot'):
self.subplot = self.figure.add_subplot(111)
self.subplot.clear()
# nothing to plot?
if len(self.points)==0:
logging.warn('No data to plot.')
return
self.subplot.boxplot(self.points, sym='k.')
if len(self.points) > 1:
self.figure.autofmt_xdate()
self.subplot.set_xticklabels(self.xlabels)
self.reset_toolbar()
if ignored == 0:
logging.info('Boxplot: Plotted %s points.'%(sum(map(len, self.points))))
else:
logging.warn('Boxplot: Plotted %s points. Ignored %s NaNs.'
%(sum(map(len, self.points)), ignored))
def set_x_axis_label(self, label):
self.subplot.set_xlabel(label)
def set_y_axis_label(self, label):
self.subplot.set_ylabel(label)
def get_point_lists(self):
return self.points
def get_xlabels(self):
return self.xlabels
def get_toolbar(self):
if not self.navtoolbar:
self.navtoolbar = NavigationToolbar(self.canvas)
self.navtoolbar.DeleteToolByPos(6)
return self.navtoolbar
def reset_toolbar(self):
# Cheat since there is no way reset
if self.navtoolbar:
self.navtoolbar._nav_stack.clear()
self.navtoolbar.push_current()
class DensityPanel(FigureCanvasWxAgg):
def __init__(self, parent, **kwargs):
self.figure = Figure()
FigureCanvasWxAgg.__init__(self, parent, -1, self.figure, **kwargs)
self.canvas = self.figure.canvas
self.SetMinSize((100, 100))
self.figure.set_facecolor((1, 1, 1))
self.figure.set_edgecolor((1, 1, 1))
self.canvas.SetBackgroundColour('white')
self.subplot = self.figure.add_subplot(111)
self.gate_helper = GatingHelper(self.subplot, self)
self.navtoolbar = None
self.point_list = []
self.gridsize = 50
self.cb = None
self.x_scale = LINEAR_SCALE
self.y_scale = LINEAR_SCALE
self.color_scale = None
self.x_label = ''
self.y_label = ''
self.cmap = 'jet'
self.canvas.mpl_connect('button_release_event', self.on_release)
def setpointslists(self, points):
self.subplot.clear()
self.point_list = points
plot_pts = np.array(points).astype(float)
if self.x_scale == LOG_SCALE:
plot_pts = plot_pts[(plot_pts[:, 0] > 0)]
if self.y_scale == LOG_SCALE:
plot_pts = plot_pts[(plot_pts[:, 1] > 0)]
hb = self.subplot.hexbin(plot_pts[:, 0],
plot_pts[:, 1],
gridsize=self.gridsize,
xscale=self.x_scale,
yscale=self.y_scale,
bins=self.color_scale,
cmap=matplotlib.cm.get_cmap(self.cmap))
if self.cb:
# Remove the existing colorbar and reclaim the space so when we add
# a colorbar to the new hexbin subplot, it doesn't get indented.
self.figure.delaxes(self.figure.axes[1])
self.figure.subplots_adjust(right=0.90)
self.cb = self.figure.colorbar(hb)
if self.color_scale == LOG_SCALE:
self.cb.set_label('log10(N)')
self.subplot.set_xlabel(self.x_label)
self.subplot.set_ylabel(self.y_label)
xmin = np.nanmin(plot_pts[:, 0])
xmax = np.nanmax(plot_pts[:, 0])
ymin = np.nanmin(plot_pts[:, 1])
ymax = np.nanmax(plot_pts[:, 1])
# Pad all sides
if self.x_scale == LOG_SCALE:
xmin = xmin / 1.5
xmax = xmax * 1.5
else:
xmin = xmin - (xmax - xmin) / 20.
xmax = xmax + (xmax - xmin) / 20.
if self.y_scale == LOG_SCALE:
ymin = ymin / 1.5
ymax = ymax * 1.5
else:
ymin = ymin - (ymax - ymin) / 20.
ymax = ymax + (ymax - ymin) / 20.
self.subplot.axis([xmin, xmax, ymin, ymax])
self.reset_toolbar()
def getpointslists(self):
return self.point_list
def setgridsize(self, gridsize):
self.gridsize = gridsize
def set_x_scale(self, scale):
self.x_scale = scale
def set_y_scale(self, scale):
self.y_scale = scale
def set_color_scale(self, scale):
if scale == LINEAR_SCALE:
scale = None
self.color_scale = scale
def set_x_label(self, label):
self.x_label = label
def set_y_label(self, label):
self.y_label = label
def set_colormap(self, cmap):
self.cmap = cmap
self.draw()
def get_toolbar(self):
if not self.navtoolbar:
self.navtoolbar = NavigationToolbar(self.canvas)
return self.navtoolbar
def reset_toolbar(self):
# Cheat since there is no way reset
if self.navtoolbar:
self.navtoolbar._views.clear()
self.navtoolbar._positions.clear()
self.navtoolbar.push_current()
def set_configpanel(self, configpanel):
'''Allow access of the control panel from the plotting panel'''
self.configpanel = configpanel
def on_release(self, evt):
if evt.button == 3: # right click
self.show_popup_menu((evt.x, self.canvas.GetSize()[1] - evt.y),
None)
def show_popup_menu(self, (x, y), data):
self.popup_menu_filters = {}
popup = wx.Menu()
loadimages_table_item = popup.Append(
-1, 'Create gated table for CellProfiler LoadImages')
selected_gate = self.configpanel.gate_choice.get_gatename_or_none()
selected_gates = []
if selected_gate:
selected_gates = [selected_gate]
self.Bind(
wx.EVT_MENU, lambda (e): ui.prompt_user_to_create_loadimages_table(
self, selected_gates), loadimages_table_item)
show_images_in_gate_item = popup.Append(-1, 'Show images in gate')
show_images_in_gate_item.Enable(selected_gate is not None)
self.Bind(wx.EVT_MENU, self.show_images_from_gate,
show_images_in_gate_item)
if p.object_table:
show_objects_in_gate_item = popup.Append(
-1, 'Show %s in gate' % (p.object_name[1]))
show_objects_in_gate_item.Enable(selected_gate is not None)
self.Bind(wx.EVT_MENU, self.show_objects_from_gate,
show_objects_in_gate_item)
self.PopupMenu(popup, (x, y))
class HistogramPanel(FigureCanvasWxAgg):
def __init__(self, parent, points, bins=100, **kwargs):
self.figure = Figure()
FigureCanvasWxAgg.__init__(self, parent, -1, self.figure, **kwargs)
self.canvas = self.figure.canvas
self.SetMinSize((100, 100))
self.figure.set_facecolor((1, 1, 1))
self.figure.set_edgecolor((1, 1, 1))
self.canvas.SetBackgroundColour('white')
self.subplot = self.figure.add_subplot(111)
self.gate_helper = GatingHelper(self.subplot, self)
self.navtoolbar = NavigationToolbar(self.canvas)
#self.navtoolbar.Realize()
self.x_label = ''
self.log_y = False
self.x_scale = LINEAR_SCALE
self.setpoints(points, bins)
self.canvas.mpl_connect('button_release_event', self.on_release)
def setpoints(self, points, bins):
''' Updates the data to be plotted and redraws the plot.
points - array of samples
bins - number of bins to aggregate points in
'''
points = np.array(points).astype('f')
self.bins = bins
x_label = self.x_label
self.subplot.clear()
# log xform the data, ignoring non-positives
# XXX: This will not work for selection since the data is changed
if self.x_scale in [LOG_SCALE, LOG2_SCALE]:
if self.x_scale == LOG_SCALE:
points = np.log(points[points > 0])
x_label = 'Log(%s)' % (self.x_label)
elif self.x_scale == LOG2_SCALE:
points = np.log2(points[points > 0])
x_label = 'Log2(%s)' % (self.x_label)
ignored = len(points[points <= 0])
if ignored > 0:
logging.warn('Histogram ignored %s negative value%s.' %
(ignored, (ignored != 1 and 's' or '')))
# hist apparently doesn't like nans, need to preen them out first
points = points[~np.isnan(points)]
# nothing to plot?
if len(points) == 0:
logging.warn('No data to plot.')
return
self.subplot.hist(points,
self.bins,
facecolor=[0.0, 0.62, 1.0],
edgecolor='none',
log=self.log_y,
alpha=0.75)
self.subplot.set_xlabel(x_label)
self.reset_toolbar()
def set_x_label(self, label):
self.x_label = label
def set_x_scale(self, scale):
'''scale -- LINEAR_SCALE, LOG_SCALE, or LOG2_SCALE'''
self.x_scale = scale
def set_y_scale(self, scale):
'''scale -- LINEAR_SCALE or LOG_SCALE'''
if scale == LINEAR_SCALE:
self.log_y = False
elif scale == LOG_SCALE:
self.log_y = True
else:
raise ValueError('Unsupported y-axis scale.')
def get_toolbar(self):
return self.navtoolbar
def reset_toolbar(self):
'''Clears the navigation toolbar history. Called after setpoints.'''
# Cheat since there is no way reset
if self.navtoolbar:
self.navtoolbar._views.clear()
self.navtoolbar._positions.clear()
self.navtoolbar.push_current()
def set_configpanel(self, configpanel):
'''Allow access of the control panel from the plotting panel'''
self.configpanel = configpanel
def on_release(self, evt):
'''click handler'''
if evt.button == 3: # right click
self.show_popup_menu((evt.x, self.canvas.GetSize()[1] - evt.y),
None)
def show_popup_menu(self, (x, y), data):
'''Show context sensitive popup menu.'''
self.popup_menu_filters = {}
popup = wx.Menu()
loadimages_table_item = popup.Append(
-1, 'Create gated table for CellProfiler LoadImages')
selected_gate = self.configpanel.gate_choice.get_gatename_or_none()
selected_gates = []
if selected_gate:
selected_gates = [selected_gate]
self.Bind(
wx.EVT_MENU, lambda (e): ui.prompt_user_to_create_loadimages_table(
self, selected_gates), loadimages_table_item)
show_images_in_gate_item = popup.Append(-1, 'Show images in gate')
show_images_in_gate_item.Enable(selected_gate is not None)
self.Bind(wx.EVT_MENU, self.show_images_from_gate,
show_images_in_gate_item)
if p.object_table:
show_objects_in_gate_item = popup.Append(
-1, 'Show %s in gate (montage)' % (p.object_name[1]))
show_objects_in_gate_item.Enable(selected_gate is not None)
self.Bind(wx.EVT_MENU, self.show_objects_from_gate,
show_objects_in_gate_item)
self.PopupMenu(popup, (x, y))
