Merge remote-tracking branch 'upstream/RELEASE_next_minor' into RELEA…

…SE_v1.1

doc/citing.rst

@@ -8,37 +8,36 @@ entry
 
 .. code-block:: bibtex
 
-    @misc{francisco_de_la_pena_2015_27735,
-      author       = {Francisco de la Peña and
-                      Vidar Tonaas Fauske and
-                      Pierre Burdet and
-                      Tomas Ostasevicius and
-                      Mike Sarahan and
-                      Magnus Nord and
-                      Joshua A. Taillon and
-                      Duncan Johnstone and
-                      Katherine E. MacArthur and
-                      Alberto Eljarrat and
-                      Stefano Mazzucco and
-                      Jan Caron and
-                      Tom Furnival and
-                      Michael Walls and
-                      Eric Prestat and
-                      Gaël Donval and
-                      Ben Martineau and
-                      Luiz Fernando Zagonel and
-                      Petras Jokubauskas and
-                      Thomas Aarholt and
-                      and Andreas Garmannslund and
-                      Ilya Iyengar and
-                      },
-      title        = {hyperspy: HyperSpy 0.8.5},
-      month        = jun,
-      year         = 2016,
-      doi          = {10.5281/zenodo.58841},
-      url          = {http://dx.doi.org/10.5281/zenodo.58841}
-    }
-
+   @misc{francisco_de_la_pena_2016_58841,
+     author       = {Francisco de la Peña and
+                     Tomas Ostasevicius and
+                     Vidar Tonaas Fauske and
+                     Pierre Burdet and
+                     Petras Jokubauskas and
+                     Mike Sarahan and
+                     Duncan Johnstone and
+                     Magnus Nord and
+                     Josh Taillon and
+                     Jan Caron and
+                     Katherine E. MacArthur and
+                     Alberto Eljarrat and
+                     Stefano Mazzucco and
+                     Tom Furnival and
+                     Eric Prestat and
+                     Michael Walls and
+                     Gaël Donval and
+                     Ben Martineau and
+                     Luiz Fernando Zagonel and
+                     Andreas Garmannslund and
+                     Thomas Aarholt and
+                     Christoph Gohlke and
+                     Ilya Iyengar},
+     title        = {hyperspy: HyperSpy 1.0.1},
+     month        = jul,
+     year         = 2016,
+     doi          = {10.5281/zenodo.58841},
+     url          = {http://dx.doi.org/10.5281/zenodo.58841}
+   }
 
 or click on the DOI badge below for more citation formats.
 

hyperspy/_components/eels_cl_edge.py

@@ -306,6 +306,15 @@ def function(self, E):
         """Returns the number of counts in barns
 
         """
+        shift = self.onset_energy.value - self.GOS.onset_energy
+        if shift != self.GOS.energy_shift:
+            # Because hspy Events are not executed in any given order,
+            # an external function could be in the same event execution list
+            # as _integrate_GOS and be executed first. That can potentially
+            # cause an error that enforcing _integrate_GOS here prevents. Note
+            # that this is suboptimal because _integrate_GOS is computed twice
+            # unnecessarily.
+            self._integrate_GOS()
         Emax = self.GOS.energy_axis[-1] + self.GOS.energy_shift
         cts = np.zeros((len(E)))
         bsignal = (E >= self.onset_energy.value)

hyperspy/_signals/eels.py

@@ -170,12 +170,11 @@ def estimate_zero_loss_peak_centre(self, mask=None):
         self._check_signal_dimension_equals_one()
         self._check_navigation_mask(mask)
         zlpc = self.valuemax(-1)
-        if self.axes_manager.navigation_dimension == 1:
-            zlpc = zlpc.as_signal1D(0)
-        elif self.axes_manager.navigation_dimension > 1:
-            zlpc = zlpc.as_signal2D((0, 1))
         if mask is not None:
             zlpc.data[mask.data] = np.nan
+        zlpc.set_signal_type("")
+        title = self.metadata.General.title
+        zlpc.metadata.General.title = "ZLP(%s)" % title
         return zlpc
 
     def align_zero_loss_peak(
@@ -337,20 +336,22 @@ def estimate_elastic_scattering_intensity(
         if isinstance(threshold, numbers.Number):
             I0 = self.isig[:threshold].integrate1D(-1)
         else:
-            I0 = self._get_navigation_signal().transpose(signal_axes=0)
-            for i, s in progressbar(enumerate(self),
-                                    total=self.axes_manager.navigation_size,
-                                    disable=not show_progressbar,
-                                    leave=True):
-                threshold_ = threshold.isig[I0.axes_manager.indices].data[0]
-                if np.isnan(threshold_):
-                    s.data[:] = np.nan
-                else:
-                    s.data[:] = (self.inav[I0.axes_manager.indices].isig[
-                                 :threshold_].integrate1D(-1).data)
-        I0 = I0.transpose(signal_axes=self.axes_manager.navigation_dimension)
+            I0 = self._get_navigation_signal()
+            I0.axes_manager.set_signal_dimension(0)
+            with progressbar(total=self.axes_manager.navigation_size,
+                             disable=not show_progressbar,
+                             leave=True) as pbar:
+                for i, (i0, th, s) in enumerate(zip(I0._iterate_signal(),
+                                                    threshold._iterate_signal(),
+                                                    self)):
+                    if np.isnan(th[0]):
+                        i0[:] = np.nan
+                    else:
+                        i0[:] = s.isig[:th[0]].integrate1D(-1).data
+                    pbar.update(1)
         I0.metadata.General.title = (
             self.metadata.General.title + ' elastic intensity')
+        I0.set_signal_type("")
         if self.tmp_parameters.has_item('filename'):
             I0.tmp_parameters.filename = (
                 self.tmp_parameters.filename +
@@ -461,16 +462,15 @@ def estimate_elastic_scattering_threshold(self,
         # Create spectrum image, stop and return value
         threshold.metadata.General.title = (
             self.metadata.General.title +
-            ' ZLP threshold')
+            ' elastic scattering threshold')
         if self.tmp_parameters.has_item('filename'):
             threshold.tmp_parameters.filename = (
                 self.tmp_parameters.filename +
-                '_ZLP_threshold')
+                '_elastic_scattering_threshold')
             threshold.tmp_parameters.folder = self.tmp_parameters.folder
             threshold.tmp_parameters.extension = \
                 self.tmp_parameters.extension
-        threshold = threshold.transpose(signal_axes=min(
-            2, self.axes_manager.navigation_dimension))
+        threshold.set_signal_type("")
         return threshold
 
     def estimate_thickness(self,
@@ -532,6 +532,8 @@ def estimate_thickness(self,
             s.tmp_parameters.folder = self.tmp_parameters.folder
             s.tmp_parameters.extension = \
                 self.tmp_parameters.extension
+        s.axes_manager.set_signal_dimension(0)
+        s.set_signal_type("")
         return s
 
     def fourier_log_deconvolution(self,

hyperspy/_signals/signal1d.py

@@ -1221,6 +1221,9 @@ def estimate_peak_width(self,
             right.metadata.General.title = (
                 self.metadata.General.title +
                 " full-width at %.1f maximum right position" % factor)
+        for signal in (left, width, right):
+            signal.axes_manager.set_signal_dimension(0)
+            signal.set_signal_type("")
         if return_interval is True:
             return [width, left, right]
         else:

hyperspy/axes.py

@@ -28,7 +28,6 @@
 from hyperspy.misc.math_tools import isfloat
 
 import warnings
-from hyperspy.exceptions import VisibleDeprecationWarning
 
 
 class ndindex_nat(np.ndindex):
@@ -312,22 +311,6 @@ def __repr__(self):
     def __str__(self):
         return self._get_name() + " axis"
 
-    def connect(self, f):
-        warnings.warn(
-            "The method `DataAxis.connect()` has been deprecated and will "
-            "be removed in HyperSpy 0.10. Please use "
-            "`DataAxis.events.value_changed.connect()` instead.",
-            VisibleDeprecationWarning)
-        self.events.value_changed.connect(f, [])
-
-    def disconnect(self, f):
-        warnings.warn(
-            "The method `DataAxis.disconnect()` has been deprecated and "
-            "will be removed in HyperSpy 0.10. Please use "
-            "`DataAxis.events.indices_changed.disconnect()` instead.",
-            VisibleDeprecationWarning)
-        self.events.value_changed.disconnect(f)
-
     def update_index_bounds(self):
         self.high_index = self.size - 1
 
@@ -406,14 +389,6 @@ def value2index(self, value, rounding=round):
             else:
                 raise ValueError("The value is out of the axis limits")
 
-    def set_index_from_value(self, value):
-        warnings.warn(
-            "The method `DataAxis.set_index_from_value()` has been deprecated "
-            "and will be removed in HyperSpy 0.10. Please set the value using "
-            "the `value` attribute and the index will update automatically.",
-            VisibleDeprecationWarning)
-        self.value = value
-
     def index2value(self, index):
         if isinstance(index, np.ndarray):
             return self.axis[index.ravel()].reshape(index.shape)
@@ -861,7 +836,7 @@ def update_axes_attributes_from(self, axes,
             self.events.any_axis_changed.trigger(obj=self)
 
     def _update_attributes(self):
-        getitem_tuple = ()
+        getitem_tuple = []
         values = []
         self.signal_axes = ()
         self.navigation_axes = ()
@@ -876,10 +851,12 @@ def _update_attributes(self):
             else:
                 getitem_tuple += axis.slice,
                 self.signal_axes += axis,
+        if not self.signal_axes and self.navigation_axes:
+            getitem_tuple[-1] = slice(axis.index, axis.index + 1)
 
         self.signal_axes = self.signal_axes[::-1]
         self.navigation_axes = self.navigation_axes[::-1]
-        self._getitem_tuple = getitem_tuple
+        self._getitem_tuple = tuple(getitem_tuple)
         self.signal_dimension = len(self.signal_axes)
         self.navigation_dimension = len(self.navigation_axes)
         if self.navigation_dimension != 0:
@@ -929,22 +906,6 @@ def set_signal_dimension(self, value):
         for axis in self._axes:
             axis.navigate = tl.pop(0)
 
-    def connect(self, f):
-        warnings.warn(
-            "The method `AxesManager.connect()` has been deprecated and will "
-            "be removed in HyperSpy 0.10. Please use "
-            "`AxesManager.events.indices_changed.connect()` instead.",
-            VisibleDeprecationWarning)
-        self.events.indices_changed.connect(f, [])
-
-    def disconnect(self, f):
-        warnings.warn(
-            "The method `AxesManager.disconnect()` has been deprecated and "
-            "will be removed in HyperSpy 0.10. Please use "
-            "`AxesManager.events.indices_changed.disconnect()` instead.",
-            VisibleDeprecationWarning)
-        self.events.indices_changed.disconnect(f)
-
     def key_navigator(self, event):
         if len(self.navigation_axes) not in (1, 2):
             return

hyperspy/component.py

@@ -33,7 +33,6 @@
 from hyperspy.misc.export_dictionary import export_to_dictionary, \
     load_from_dictionary
 from hyperspy.events import Events, Event
-from hyperspy.exceptions import VisibleDeprecationWarning
 
 import logging
 
@@ -200,22 +199,6 @@ def __repr__(self):
     def __len__(self):
         return self._number_of_elements
 
-    def connect(self, f):
-        warnings.warn(
-            "The method `Parameter.connect()` has been deprecated and will be "
-            "removed in HyperSpy 0.10. Please use "
-            "`Parameter.events.value_changed.connect()` instead.",
-            VisibleDeprecationWarning)
-        self.events.value_changed.connect(f, [])
-
-    def disconnect(self, f):
-        warnings.warn(
-            "The method `Parameter.disconnect()` has been deprecated and will "
-            "be removed in HyperSpy 0.10. Please use "
-            "`Parameter.events.value_changed.disconnect()` instead.",
-            VisibleDeprecationWarning)
-        self.events.value_changed.disconnect(f)
-
     def _get_value(self):
         if self.twin is None:
             return self.__value
@@ -839,22 +822,6 @@ def _axes_manager(self, value):
             parameter._axes_manager = value
         self.__axes_manager = value
 
-    def connect(self, f):
-        warnings.warn(
-            "The method `Component.connect()` has been deprecated and will be "
-            "removed in HyperSpy 0.10. Please use "
-            "`Component.events.active_changed.connect()` instead.",
-            VisibleDeprecationWarning)
-        self.events.active_changed.connect(f, [])
-
-    def disconnect(self, f):
-        warnings.warn(
-            "The method `Component.disconnect()` has been deprecated and will "
-            "be removed in HyperSpy 0.10. Please use "
-            "`Component.events.active_changed.disconnect()` instead.",
-            VisibleDeprecationWarning)
-        self.events.active_changed.disconnect(f)
-
     def _get_active(self):
         if self.active_is_multidimensional is True:
             # The following should set

hyperspy/misc/slicing.py

@@ -208,7 +208,8 @@ def _get_array_slices(self, slices, isNavigation=None):
     def _slicer(self, slices, isNavigation=None, out=None):
         array_slices = self._get_array_slices(slices, isNavigation)
         if out is None:
-            _obj = self._deepcopy_with_new_data(self.data[array_slices])
+            _obj = self._deepcopy_with_new_data(self.data[array_slices],
+                                                copy_variance=True)
             _to_remove = []
             for slice_, axis in zip(array_slices, _obj.axes_manager._axes):
                 if (isinstance(slice_, slice) or