Fix plotting windows with navigation dimension >=2 and simplify setti…

…ng background and integration windows line markers

exspy/signals/eds.py

@@ -987,7 +987,7 @@ def _plot_xray_lines(
  self.add_xray_lines_markers(xray_lines, render_figure=False)
  if background_windows is not None:
  self._add_background_windows_markers(
- background_windows, render_figure=False
+ background_windows, linestyles="--", render_figure=False
  )
  if integration_windows is not None:
  if integration_windows == "auto":
@@ -997,7 +997,7 @@ def _plot_xray_lines(
  windows_width=integration_windows, xray_lines=xray_lines
  )
  self._add_vertical_lines_groups(
- integration_windows, linestyle="--", render_figure=False
+ integration_windows, render_figure=False
  )
  # Render figure only at the end
  if render_figure:
@@ -1012,16 +1012,22 @@ def _add_vertical_lines_groups(self, position, render_figure=True, **kwargs):
  position: 2D array of float
  The position on the signal axis. Each row corresponds to a
  group.
- kwargs
+ **kwargs : dict
  keywords argument for :class:`hyperspy.api.plot.markers.VerticalLine`
  """
- colors = itertools.cycle(
+ position = np.array(position)
+ length = position.shape[1]
+ colors_cycle = itertools.cycle(
  np.sort(plt.rcParams["axes.prop_cycle"].by_key()["color"])
  )
+ colors = np.array(
+ [[c] * length for c, w in zip(colors_cycle, position)]
+ ).flatten()
 
- for x, color in zip(position, colors):
- line = hs.plot.markers.VerticalLines(offsets=x, color=color, **kwargs)
- self.add_marker(line, render_figure=False)
+ line = hs.plot.markers.VerticalLines(
+ offsets=position.flatten(), color=colors, **kwargs
+ )
+ self.add_marker(line, render_figure=False)
  if render_figure:
  self._render_figure(plot=["signal_plot"])
 
@@ -1102,7 +1108,9 @@ def remove_xray_lines_markers(self, xray_lines, render_figure=True):
  if render_figure:
  self._render_figure(plot=["signal_plot"])
 
- def _add_background_windows_markers(self, windows_position, render_figure=True):
+ def _add_background_windows_markers(
+ self, windows_position, render_figure=True, **kwargs
+ ):
  """
  Plot the background windows associated with each X-ray lines.
 
@@ -1121,21 +1129,50 @@ def _add_background_windows_markers(self, windows_position, render_figure=True):
  --------
  estimate_background_windows, get_lines_intensity
  """
- self._add_vertical_lines_groups(windows_position)
- segments = []
- for bw in windows_position:
+ self._add_vertical_lines_groups(windows_position, **kwargs)
+
+ # Calculate the start and end of segments for each window
+ # nav_dim + (number of x-ray lines, vertices positions)
+ # vertices positions are (x0, y0), (x1, x2)
+ segments_ = np.zeros(
+ self.axes_manager.navigation_shape + (len(windows_position), 2, 2)
+ )
+
+ for i, bw in enumerate(windows_position):
+ # Check that all background windows are within the energy range
  if any(v < self.axes_manager[-1].low_value for v in bw) or any(
  v > self.axes_manager[-1].high_value for v in bw
  ):
  raise ValueError("Background windows is outside of the signal range.")
- y1 = self.isig[bw[0] : bw[1]].mean(-1).data
- y2 = self.isig[bw[2] : bw[3]].mean(-1).data
- x1 = (bw[0] + bw[1]) / 2.0
- x2 = (bw[2] + bw[3]) / 2.0
- segments.append([[x1, y1[0]], [x2, y2[0]]])
- segments = np.array(segments)
- lines = hs.plot.markers.Lines(segments=segments, color="black")
+
+ # calculate the position of the segments
+ y0 = self.isig[bw[0] : bw[1]].mean(-1).data
+ y1 = self.isig[bw[2] : bw[3]].mean(-1).data
+ x0 = (bw[0] + bw[1]) / 2.0
+ x1 = (bw[2] + bw[3]) / 2.0
+
+ segments_[..., i, 0, 0] = x0
+ segments_[..., i, 0, 1] = y0.T
+ segments_[..., i, 1, 0] = x1
+ segments_[..., i, 1, 1] = y1.T
+
+ # convert to ragged array to comply with requirement for
+ # navigation position dependent markers
+ # 2000 x 2000 navigation shape takes ~2s
+ # 1000 x 1000 navigation shape takes ~0.5s
+ # 500 x 500 navigation shape takes ~0.01s
+ segments = np.empty(self.axes_manager.navigation_shape, dtype=object)
+ for i in np.ndindex(self.axes_manager.navigation_shape):
+ segments[i] = segments_[i]
+
+ colors_cycle = itertools.cycle(
+ np.sort(plt.rcParams["axes.prop_cycle"].by_key()["color"])
+ )
+ colors = np.array([c for c, w in zip(colors_cycle, windows_position)]).flatten()
+
+ lines = hs.plot.markers.Lines(segments=segments, color=colors, **kwargs)
  self.add_marker(lines, render_figure=False)
+
  if render_figure:
  self._render_figure(plot=["signal_plot"])
 

exspy/tests/signals/test_eds_tem.py

@@ -21,6 +21,7 @@
 import numpy as np
 import pytest
 
+import hyperspy.api as hs
 from hyperspy.components1d import Gaussian
 from hyperspy.decorators import lazifyTestClass
 
@@ -607,6 +608,23 @@ def test_outside_range_background_windows(self):
  s.isig[2.0:].plot(True, background_windows=bw)
 
 
+def test_plot_windows():
+ s = exspy.data.EDS_TEM_FePt_nanoparticles()
+
+ rng = np.random.default_rng()
+
+ [s * v * 10 for v in rng.random((10))]
+
+ s = hs.stack([s * v * 10 for v in rng.random((10))])
+ s = hs.stack([s * v * 10 for v in rng.random((5))])
+
+ bw = s.estimate_background_windows(line_width=[5.0, 2.0])
+ iw = s.estimate_integration_windows(windows_width=3)
+
+ s.plot(True, background_windows=bw, integration_windows=iw)
+ s.axes_manager.indices = (1, 2)
+
+
 def test_with_signals_examples():
  sig = exspy.data.EDS_TEM_FePt_nanoparticles()
  for s in (sig, sig.as_lazy()):