def plot_signal(self):
if self.signal_plot is not None:
self.signal_plot.plot()
return
# Create the figure
self.xlabel = '%s' % str(self.axes_manager.signal_axes[0])
if self.axes_manager.signal_axes[0].units is not Undefined:
self.xlabel += ' (%s)' % self.axes_manager.signal_axes[0].units
self.ylabel = self.quantity_label
self.axis = self.axes_manager.signal_axes[0]
sf = signal1d.Signal1DFigure(title=self.signal_title + " Signal")
sf.xlabel = self.xlabel
sf.ylabel = self.ylabel
sf.axis = self.axis
if sf.ax is None:
sf.create_axis()
sf.axes_manager = self.axes_manager
self.signal_plot = sf
# Create a line to the left axis with the default indices
sl = signal1d.Signal1DLine()
is_complex = np.iscomplexobj(self.signal_data_function())
sl.autoscale = True if not is_complex else False
sl.data_function = self.signal_data_function
sl.plot_indices = True
if self.pointer is not None:
color = self.pointer.color
else:
color = 'red'
sl.set_line_properties(color=color, type='step')
# Add the line to the figure:
sf.add_line(sl)
# If the data is complex create a line in the left axis with the
# default coordinates
if is_complex:
sl = signal1d.Signal1DLine()
sl.autoscale = True
sl.data_function = self.signal_data_function
sl.plot_coordinates = True
sl._plot_imag = True
sl.set_line_properties(color="blue", type='step')
# Add extra line to the figure
sf.add_line(sl)
self.signal_plot = sf
sf.plot()
if sf.figure is not None:
if self.axes_manager.navigation_axes:
self.signal_plot.figure.canvas.mpl_connect(
'key_press_event', self.axes_manager.key_navigator)
if self.navigator_plot is not None:
self.navigator_plot.events.closed.connect(
self._on_navigator_plot_closing, [])
sf.events.closed.connect(self.close_navigator_plot, [])
self.signal_plot.figure.canvas.mpl_connect(
'key_press_event', self.key2switch_right_pointer)
self.navigator_plot.figure.canvas.mpl_connect(
'key_press_event', self.key2switch_right_pointer)
self.navigator_plot.figure.canvas.mpl_connect(
'key_press_event', self.axes_manager.key_navigator)
def add_right_pointer(self):
if self.signal_plot.right_axes_manager is None:
self.signal_plot.right_axes_manager = \
copy.deepcopy(self.axes_manager)
if self.right_pointer is None:
pointer = self.assign_pointer()
self.right_pointer = pointer(self.signal_plot.right_axes_manager)
# The following is necessary because e.g. a line pointer does not
# have size
if hasattr(self.pointer, "size"):
self.right_pointer.size = self.pointer.size
self.right_pointer.color = 'blue'
self.right_pointer.connect_navigate()
self.right_pointer.set_mpl_ax(self.navigator_plot.ax)
if self.right_pointer is not None:
for axis in self.axes_manager.navigation_axes[self.
_pointer_nav_dim:]:
self.signal_plot.right_axes_manager._axes[
axis.index_in_array] = axis
rl = signal1d.Signal1DLine()
rl.autoscale = True
rl.data_function = self.signal_data_function
rl.set_line_properties(color=self.right_pointer.color, type='step')
self.signal_plot.create_right_axis()
self.signal_plot.add_line(rl, ax='right')
rl.plot_indices = True
rl.text_position = (
1.,
1.05,
)
rl.plot()
self.right_pointer_on = True
def add_right_pointer(self, **kwargs):
if self.signal_plot.right_axes_manager is None:
self.signal_plot.right_axes_manager = \
copy.deepcopy(self.axes_manager)
if self.right_pointer is None:
pointer = self.assign_pointer()
self.right_pointer = pointer(self.signal_plot.right_axes_manager)
# The following is necessary because e.g. a line pointer does not
# have size
if hasattr(self.pointer, "size"):
self.right_pointer.size = self.pointer.size
self.right_pointer.color = 'blue'
self.right_pointer.connect_navigate()
self.right_pointer.set_mpl_ax(self.navigator_plot.ax)
if self.right_pointer is not None:
for axis in self.axes_manager.navigation_axes[self.
_pointer_nav_dim:]:
self.signal_plot.right_axes_manager._axes[
axis.index_in_array] = axis
rl = signal1d.Signal1DLine()
rl.data_function = self.signal_data_function
rl.set_line_properties(color=self.right_pointer.color, type='step')
self.signal_plot.create_right_axis()
self.signal_plot.add_line(rl, ax='right', connect_navigation=True)
rl.plot_indices = True
rl.text_position = (
1.,
1.05,
)
rl.plot(**kwargs)
self.right_pointer_on = True
# because we added the right axis, we need to redraw the canvas to
# update the background
self.signal_plot.figure.canvas.draw_idle()
def add_right_pointer(self, **kwargs):
if self.signal_plot.right_axes_manager is None:
self.signal_plot.right_axes_manager = \
copy.deepcopy(self.axes_manager)
if self.right_pointer is None:
pointer = self.assign_pointer()
self.right_pointer = pointer(self.signal_plot.right_axes_manager)
# The following is necessary because e.g. a line pointer does not
# have size
if hasattr(self.pointer, "size"):
self.right_pointer.size = self.pointer.size
self.right_pointer.color = 'blue'
self.right_pointer.connect_navigate()
self.right_pointer.set_mpl_ax(self.navigator_plot.ax)
if self.right_pointer is not None:
for axis in self.axes_manager.navigation_axes[self.
_pointer_nav_dim:]:
self.signal_plot.right_axes_manager._axes[
axis.index_in_array] = axis
rl = signal1d.Signal1DLine()
rl.data_function = self.signal_data_function
rl.set_line_properties(color=self.right_pointer.color, type='step')
self.signal_plot.create_right_axis()
self.signal_plot.add_line(rl, ax='right', connect_navigation=True)
rl.plot_indices = True
rl.text_position = (
1.,
1.05,
)
rl.plot(**kwargs)
self.right_pointer_on = True
if hasattr(self.signal_plot.figure, 'tight_layout'):
try:
self.signal_plot.figure.tight_layout()
except BaseException:
# tight_layout is a bit brittle, we do this just in case it
# complains
pass
def plot_navigator(self,
colorbar=True,
scalebar=True,
scalebar_color="white",
axes_ticks=None,
saturated_pixels=None,
vmin=None,
vmax=None,
no_nans=False,
centre_colormap="auto",
title=None,
min_aspect=0.1,
**kwds):
if self.axes_manager.navigation_dimension == 0:
return
if self.navigator_data_function is None:
return
if self.navigator_data_function == "slider":
self._get_navigation_sliders()
return
title = title or self.signal_title + " Navigator" if self.signal_title else ""
if self.navigator_plot is not None:
self.navigator_plot.plot()
return
elif len(self.navigator_data_function().shape) == 1:
# Create the figure
sf = signal1d.Signal1DFigure(title=title)
axis = self.axes_manager.navigation_axes[0]
sf.xlabel = '%s' % str(axis)
if axis.units is not Undefined:
sf.xlabel += ' (%s)' % axis.units
sf.ylabel = r'$\Sigma\mathrm{data\,over\,all\,other\,axes}$'
sf.axis = axis
sf.axes_manager = self.axes_manager
self.navigator_plot = sf
# Create a line to the left axis with the default
# indices
sl = signal1d.Signal1DLine()
sl.data_function = self.navigator_data_function
sl.set_line_properties(color='blue', type='step')
# Add the line to the figure
sf.add_line(sl)
sf.plot()
self.pointer.set_mpl_ax(sf.ax)
if self.axes_manager.navigation_dimension > 1:
self._get_navigation_sliders()
for axis in self.axes_manager.navigation_axes[:-2]:
axis.events.index_changed.connect(sf.update, [])
sf.events.closed.connect(
partial(axis.events.index_changed.disconnect,
sf.update), [])
self.navigator_plot = sf
elif len(self.navigator_data_function().shape) >= 2:
imf = image.ImagePlot()
imf.data_function = self.navigator_data_function
imf.colorbar = colorbar
imf.scalebar = scalebar
imf.scalebar_color = scalebar_color
imf.axes_ticks = axes_ticks
imf.saturated_pixels = saturated_pixels
imf.vmin = vmin
imf.vmax = vmax
imf.no_nans = no_nans
imf.centre_colormap = centre_colormap
imf.min_aspect = min_aspect
# Navigator labels
if self.axes_manager.navigation_dimension == 1:
imf.yaxis = self.axes_manager.navigation_axes[0]
imf.xaxis = self.axes_manager.signal_axes[0]
elif self.axes_manager.navigation_dimension >= 2:
imf.yaxis = self.axes_manager.navigation_axes[1]
imf.xaxis = self.axes_manager.navigation_axes[0]
if self.axes_manager.navigation_dimension > 2:
self._get_navigation_sliders()
for axis in self.axes_manager.navigation_axes[2:]:
axis.events.index_changed.connect(imf.update, [])
imf.events.closed.connect(
partial(axis.events.index_changed.disconnect,
imf.update), [])
imf.title = title
if "cmap" not in kwds.keys() or kwds['cmap'] is None:
kwds["cmap"] = preferences.Plot.cmap_navigator
imf.plot(**kwds)
self.pointer.set_mpl_ax(imf.ax)
self.navigator_plot = imf
def plot_navigator(self, title=None, **kwargs):
"""
Parameters
----------
title : str, optional
Title of the navigator. The default is None.
**kwargs : dict
The kwargs are passed to plot method of
:py:meth:`hyperspy.drawing.image.ImagePlot` or
:py:meth:`hyperspy.drawing.signal1d.Signal1DLine`.
"""
if self.axes_manager.navigation_dimension == 0:
return
if self.navigator_data_function is None:
return
if self.navigator_data_function == "slider":
self._get_navigation_sliders()
return
title = title or self.signal_title + " Navigator" if self.signal_title else ""
if len(self.navigator_data_function().shape) == 1:
# Create the figure
sf = signal1d.Signal1DFigure(title=title)
axis = self.axes_manager.navigation_axes[0]
sf.xlabel = '%s' % str(axis)
if axis.units is not Undefined:
sf.xlabel += ' (%s)' % axis.units
sf.ylabel = r'$\Sigma\mathrm{data\,over\,all\,other\,axes}$'
sf.axis = axis
sf.axes_manager = self.axes_manager
self.navigator_plot = sf
# Create a line to the left axis with the default indices
sl = signal1d.Signal1DLine()
sl.data_function = self.navigator_data_function
# Set all kwargs value to the image figure before passing the rest
# of the kwargs to plot method of the image figure
for key in list(kwargs.keys()):
if hasattr(sl, key):
setattr(sl, key, kwargs.pop(key))
sl.set_line_properties(color='blue',
type='step')
# Add the line to the figure
sf.add_line(sl)
sf.plot()
self.pointer.set_mpl_ax(sf.ax)
if self.axes_manager.navigation_dimension > 1:
self._get_navigation_sliders()
for axis in self.axes_manager.navigation_axes[:-2]:
axis.events.index_changed.connect(sf.update, [])
sf.events.closed.connect(
partial(axis.events.index_changed.disconnect,
sf.update), [])
self.navigator_plot = sf
elif len(self.navigator_data_function().shape) >= 2:
# Create the figure
imf = image.ImagePlot(title=title)
imf.data_function = self.navigator_data_function
# Set all kwargs value to the image figure before passing the rest
# of the kwargs to plot method of the image figure
for key, value in list(kwargs.items()):
if hasattr(imf, key):
setattr(imf, key, kwargs.pop(key))
# Navigator labels
if self.axes_manager.navigation_dimension == 1:
imf.yaxis = self.axes_manager.navigation_axes[0]
imf.xaxis = self.axes_manager.signal_axes[0]
elif self.axes_manager.navigation_dimension >= 2:
imf.yaxis = self.axes_manager.navigation_axes[1]
imf.xaxis = self.axes_manager.navigation_axes[0]
if self.axes_manager.navigation_dimension > 2:
self._get_navigation_sliders()
for axis in self.axes_manager.navigation_axes[2:]:
axis.events.index_changed.connect(imf.update, [])
imf.events.closed.connect(
partial(axis.events.index_changed.disconnect,
imf.update), [])
if "cmap" not in kwargs.keys() or kwargs['cmap'] is None:
kwargs["cmap"] = preferences.Plot.cmap_navigator
imf.plot(**kwargs)
self.pointer.set_mpl_ax(imf.ax)
self.navigator_plot = imf
if self.navigator_plot is not None:
self.navigator_plot.events.closed.connect(
self._on_navigator_plot_closing, [])
def plot_navigator(self):
if self.axes_manager.navigation_dimension == 0:
return
if self.navigator_data_function is None:
return
if self.navigator_data_function is "slider":
navigation_sliders(self.axes_manager.navigation_axes,
title=self.signal_title + " navigation sliders")
return
if self.navigator_plot is not None:
self.navigator_plot.plot()
return
elif len(self.navigator_data_function().shape) == 1:
# Create the figure
sf = signal1d.Signal1DFigure(
title=self.signal_title +
' Navigator' if self.signal_title else "")
axis = self.axes_manager.navigation_axes[0]
sf.xlabel = '%s' % str(axis)
if axis.units is not Undefined:
sf.xlabel += ' (%s)' % axis.units
sf.ylabel = r'$\Sigma\mathrm{data\,over\,all\,other\,axes}$'
sf.axis = axis
sf.axes_manager = self.axes_manager
self.navigator_plot = sf
# Create a line to the left axis with the default
# indices
sl = signal1d.Signal1DLine()
sl.data_function = self.navigator_data_function
sl.set_line_properties(color='blue', type='step')
# Add the line to the figure
sf.add_line(sl)
sf.plot()
self.pointer.set_mpl_ax(sf.ax)
if self.axes_manager.navigation_dimension > 1:
navigation_sliders(self.axes_manager.navigation_axes,
title=self.signal_title +
" navigation sliders")
for axis in self.axes_manager.navigation_axes[:-2]:
axis.events.index_changed.connect(sf.update, [])
sf.events.closed.connect(
partial(axis.events.index_changed.disconnect,
sf.update), [])
self.navigator_plot = sf
elif len(self.navigator_data_function().shape) >= 2:
imf = image.ImagePlot()
imf.data_function = self.navigator_data_function
# Navigator labels
if self.axes_manager.navigation_dimension == 1:
imf.yaxis = self.axes_manager.navigation_axes[0]
imf.xaxis = self.axes_manager.signal_axes[0]
elif self.axes_manager.navigation_dimension >= 2:
imf.yaxis = self.axes_manager.navigation_axes[1]
imf.xaxis = self.axes_manager.navigation_axes[0]
if self.axes_manager.navigation_dimension > 2:
navigation_sliders(self.axes_manager.navigation_axes,
title=self.signal_title +
" navigation sliders")
for axis in self.axes_manager.navigation_axes[2:]:
axis.events.index_changed.connect(imf.update, [])
imf.events.closed.connect(
partial(axis.events.index_changed.disconnect,
imf.update), [])
imf.title = self.signal_title + ' Navigator'
imf.plot()
self.pointer.set_mpl_ax(imf.ax)
self.navigator_plot = imf
