Merge pull request #76 from ericpre/fix_active_xray_lines

`fit_background` fixes

exspy/models/edsmodel.py

@@ -180,10 +180,6 @@ def spectrum(self, value):
  "but an object of type %s was provided" % str(type(value))
  )
 
- @property
- def _active_xray_lines(self):
- return [xray_line for xray_line in self.xray_lines if xray_line.active]
-
  def add_family_lines(self, xray_lines="from_elements"):
  """Create the Xray-lines instances and configure them appropiately
 
@@ -320,13 +316,15 @@ def fix_background(self):
 
  def enable_xray_lines(self):
  """Enable the X-ray lines components."""
- for component in self.xray_lines:
- component.active = True
+ for component in self:
+ if not component.isbackground:
+ component.active = True
 
  def disable_xray_lines(self):
  """Disable the X-ray lines components."""
- for component in self._active_xray_lines:
- component.active = False
+ for component in self:
+ if not component.isbackground:
+ component.active = False
 
  def _make_position_adjuster(self, component, fix_it, show_label):
  # Override to ensure formatting of labels of xray lines
@@ -377,25 +375,31 @@ def fit_background(
  if start_energy is None:
  start_energy = self.start_energy
 
+ signal_range_mask = np.copy(self._channel_switches)
+
  # disactivate line
- self.free_background()
  with stash_active_state(self):
- self.disable_xray_lines()
- self.set_signal_range(start_energy, end_energy)
- for component in self:
- if component.isbackground is False:
- self.remove_signal_range(
- component.centre.value
- - windows_sigma[0] * component.sigma.value,
- component.centre.value
- + windows_sigma[1] * component.sigma.value,
- )
- if kind == "single":
- self.fit(**kwargs)
- if kind == "multi":
- self.multifit(**kwargs)
- self.reset_signal_range()
- self.fix_background()
+ with self.suspend_update():
+ self.free_background()
+ with stash_active_state(self):
+ self.disable_xray_lines()
+ self.set_signal_range(start_energy, end_energy)
+ for component in self:
+ if component.isbackground is False:
+ self.remove_signal_range(
+ component.centre.value
+ - windows_sigma[0] * component.sigma.value,
+ component.centre.value
+ + windows_sigma[1] * component.sigma.value,
+ )
+ if kind == "single":
+ self.fit(**kwargs)
+ if kind == "multi":
+ self.multifit(**kwargs)
+
+ # Reset previous signal range
+ self.set_signal_range_from_mask(signal_range_mask)
+ self.fix_background()
 
  def _twin_xray_lines_width(self, xray_lines):
  """
@@ -910,12 +914,8 @@ def get_lines_intensity(
  data_res = data_res[0]
  img = self.signal.isig[0:1].integrate1D(-1)
  img.data = data_res
- img.metadata.General.title = "Intensity of %s at %.2f %s from %s" % (
- xray_line,
- line_energy,
- self.signal.axes_manager.signal_axes[0].units,
- self.signal.metadata.General.title,
- )
+ units = self.signal.axes_manager.signal_axes[0].units
+ img.metadata.General.title = f"{xray_line} at {line_energy:.2f} {units}"
  img = img.transpose(signal_axes=[])
  if plot_result and img.axes_manager.signal_dimension == 0:
  print(

exspy/tests/models/test_edsmodel.py

@@ -110,6 +110,18 @@ def test_temmodel_store(self):
  self.s.set_signal_type("EDS_TEM")
  self._check_model_store()
 
+ def test_disable_xray_lines(self):
+ m = s.create_model()
+ for c in m:
+ assert c.active
+ m.disable_xray_lines()
+ assert m[0].active
+ for c in m[1:]:
+ assert not c.active
+ m.enable_xray_lines()
+ for c in m:
+ assert c.active
+
  def test_calibrate_energy_resolution(self):
  s = self.s
  m = s.create_model()

exspy/tests/models/test_linear_model.py

@@ -92,6 +92,22 @@ def test_fit_fixed_twinned_components_and_std(self):
  np.testing.assert_allclose(nonlinear_fit.data, lstsq_fit.data)
  np.testing.assert_allclose(nonlinear_std, linear_std)
 
+ def test_fit_background(self):
+ m2 = self.m2
+ m2.fit_background(optimizer="lstsq")
+ np.testing.assert_allclose(m2[0].a0.value, 11045209.18)
+
+ def test_fit_background_reset_signal_range(self):
+ m2 = self.m2
+ m2.remove_signal_range(7.0, 8.0)
+ np.testing.assert_allclose(m2._channel_switches[:200], True)
+ np.testing.assert_allclose(m2._channel_switches[301:], True)
+ np.testing.assert_allclose(m2._channel_switches[200:301], False)
+ m2.fit_background(optimizer="lstsq")
+ np.testing.assert_allclose(m2._channel_switches[:200], True)
+ np.testing.assert_allclose(m2._channel_switches[301:], True)
+ np.testing.assert_allclose(m2._channel_switches[200:301], False)
+
 
 class TestWarningSlowMultifit:
  def setup_method(self, method):

upcoming_changes/76.bugfix.rst

@@ -0,0 +1,5 @@
+:meth:`exspy.models.EDSModel.fit_background` fixes:
+
+- fix error when using linear fitting,
+- fix resetting signal range after fitting background,
+- suspend plot when fitting background.