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

…SE_next_minor

# Conflicts:
#	hyperspy/drawing/utils.py
#	hyperspy/roi.py

CHANGES.rst

@@ -17,7 +17,7 @@ Bug Fixes
 - Fix parsing EELS aperture label with unexpected value, for example 'Imaging' instead of '5 mm' (`#2772 <https://github.com/hyperspy/hyperspy/issues/2772>`_)
 - Lazy datasets can now be saved out as blockfiles (blo) (`#2774 <https://github.com/hyperspy/hyperspy/issues/2774>`_)
 - ComplexSignals can now be rebinned without error (`#2789 <https://github.com/hyperspy/hyperspy/issues/2789>`_)
-- Method `estimate_parameters` in `Polynomial` component now supports order
+- Method :py:meth:`~._components.polynomial.Polynomial.estimate_parameters` of the :py:class:`~._components.polynomial.Polynomial` component now supports order
   greater than 10 (`#2790 <https://github.com/hyperspy/hyperspy/issues/2790>`_)
 - Update minimal requirement of dependency importlib_metadata from
   >= 1.6.0 to >= 3.6 (`#2793 <https://github.com/hyperspy/hyperspy/issues/2793>`_)
@@ -48,7 +48,7 @@ Bug Fixes
 - Fix :py:meth:`~._signals.signal1d.Signal1D.shift1D`, :py:meth:`~._signals.signal1d.Signal1D.align1D` and :py:meth:`~._signals.eels.EELSSpectrum.align_zero_loss_peak` regression with navigation dimension larger than one (`#2729 <https://github.com/hyperspy/hyperspy/issues/2729>`_)
 - Fix disconnecting events when closing figure and :py:meth:`~._signals.signal1d.Signal1D.remove_background` is active (`#2734 <https://github.com/hyperspy/hyperspy/issues/2734>`_)
 - Fix :py:meth:`~.signal.BaseSignal.map` regression of lazy signal with navigation chunks of size of 1 (`#2748 <https://github.com/hyperspy/hyperspy/issues/2748>`_)
-- Fix unclear error message when reading a hspy file saved using blosc compression and `hdf5plugin` hasn't been imported previously (`#2760 <https://github.com/hyperspy/hyperspy/issues/2760>`_)
+- Fix unclear error message when reading a hspy file saved using blosc compression and ``hdf5plugin`` hasn't been imported previously (`#2760 <https://github.com/hyperspy/hyperspy/issues/2760>`_)
 - Fix saving ``navigator`` of lazy signal (`#2763 <https://github.com/hyperspy/hyperspy/issues/2763>`_)
 
 

doc/user_guide/install.rst

@@ -287,13 +287,21 @@ To get the development version from our git repository you need to install `git
 
 Installation in a Anaconda/Miniconda distribution
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+Optionally, create an environment to separate your hyperspy installation from 
+other anaconda environments (`read more about environments here 
+<https://conda.io/projects/conda/en/latest/user-guide/concepts/environments.html>`_):
+
+.. code-block:: bash
+
+    $ conda create -n hspy_dev python # create an empty environment with latest python
+    $ conda activate hspy_dev # activate environment
 
 Install the runtime and development dependencies requirements using conda:
 
 .. code-block:: bash
 
-    $ conda install hyperspy-base -c conda-forge --only-deps
-    $ conda install hyperspy-dev -c conda-forge
+    $ conda install hyperspy-base -c conda-forge --only-deps # install hyperspy dependencies
+    $ conda install hyperspy-dev -c conda-forge # install developer dependencies
 
 The package ``hyperspy-dev`` will install the development dependencies required
 for testing and building the documentation.
@@ -303,7 +311,7 @@ From the root folder of your hyperspy repository (folder containing the
 
 .. code-block:: bash
 
-    $ pip install -e . --no-deps
+    $ pip install -e . --no-deps # install the currently checked-out branch of hyperspy
 
 Installation in other (non-system) Python distribution
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/user_guide/visualisation.rst

@@ -837,9 +837,9 @@ and provide the legend labels:
     >>> import scipy.misc
     >>> s = hs.signals.Signal1D(scipy.misc.ascent()[100:160:10])
     >>> color_list = ['red', 'red', 'blue', 'blue', 'red', 'red']
-    >>> line_style_list = ['-','--','steps','-.',':','-']
+    >>> linestyle_list = ['-', '--', '-.', ':', '-']
     >>> hs.plot.plot_spectra(s, style='cascade', color=color_list,
-    >>> line_style=line_style_list,legend='auto')
+    >>>                      linestyle=linestyle_list, legend='auto')
 
 .. figure::  images/plot_spectra_color.png
   :align:   center

hyperspy/drawing/signal1d.py

@@ -91,6 +91,9 @@ def create_right_axis(self, color='black', adjust_layout=True):
             self.right_ax.hspy_fig = self
             self.right_ax.yaxis.set_animated(self.figure.canvas.supports_blit)
             self.right_ax.tick_params(axis='y', labelcolor=color)
+            # Needs to set the zorder of the ax to get the mouse event for ax
+            # See https://github.com/matplotlib/matplotlib/issues/10009
+            self.ax.set_zorder(self.right_ax.get_zorder() + 1)
         if adjust_layout:
             plt.tight_layout()
 
@@ -111,7 +114,7 @@ def close_right_axis(self, adjust_layout=True):
         if self.right_ax is not None:
             for lines in self.right_ax_lines:
                 lines.close()
-            self.right_ax.axes.get_yaxis().set_visible(False)
+            self.right_ax.remove()
             self.right_ax = None
         if adjust_layout:
             plt.tight_layout()

hyperspy/drawing/utils.py

@@ -406,50 +406,44 @@ def set_xaxis_lims(mpl_ax, hs_axis):
     mpl_ax.set_xlim(x_axis_lower_lim, x_axis_upper_lim)
 
 
-def _make_overlap_plot(spectra, ax, color="blue", line_style='-'):
-    if isinstance(color, str):
-        color = [color] * len(spectra)
-    if isinstance(line_style, str):
-        line_style = [line_style] * len(spectra)
-    for spectrum_index, (spectrum, color, line_style) in enumerate(
-            zip(spectra, color, line_style)):
+def _make_overlap_plot(spectra, ax, color, linestyle, **kwargs):
+    for spectrum_index, (spectrum, color, linestyle) in enumerate(
+            zip(spectra, color, linestyle)):
         x_axis = spectrum.axes_manager.signal_axes[0]
         spectrum = _transpose_if_required(spectrum, 1)
-        ax.plot(x_axis.axis, spectrum.data, color=color, ls=line_style)
+        ax.plot(x_axis.axis, spectrum.data, color=color, ls=linestyle,
+                **kwargs)
         set_xaxis_lims(ax, x_axis)
     _set_spectrum_xlabel(spectra, ax)
     ax.set_ylabel('Intensity')
     ax.autoscale(tight=True)
 
 
-def _make_cascade_subplot(
-        spectra, ax, color="blue", line_style='-', padding=1):
+def _make_cascade_subplot(spectra, ax, color, linestyle, padding=1, **kwargs):
     max_value = 0
     for spectrum in spectra:
         spectrum_yrange = (np.nanmax(spectrum.data) -
                            np.nanmin(spectrum.data))
         if spectrum_yrange > max_value:
             max_value = spectrum_yrange
-    if isinstance(color, str):
-        color = [color] * len(spectra)
-    if isinstance(line_style, str):
-        line_style = [line_style] * len(spectra)
-    for spectrum_index, (spectrum, color, line_style) in enumerate(
-            zip(spectra, color, line_style)):
+    for spectrum_index, (spectrum, color, linestyle) in enumerate(
+            zip(spectra, color, linestyle)):
         x_axis = spectrum.axes_manager.signal_axes[0]
         spectrum = _transpose_if_required(spectrum, 1)
         data_to_plot = ((spectrum.data - spectrum.data.min()) /
                         float(max_value) + spectrum_index * padding)
-        ax.plot(x_axis.axis, data_to_plot, color=color, ls=line_style)
+        ax.plot(x_axis.axis, data_to_plot, color=color, ls=linestyle,
+                **kwargs)
         set_xaxis_lims(ax, x_axis)
     _set_spectrum_xlabel(spectra, ax)
     ax.set_yticks([])
     ax.autoscale(tight=True)
 
 
-def _plot_spectrum(spectrum, ax, color="blue", line_style='-'):
+def _plot_spectrum(spectrum, ax, color="blue", linestyle='-', **kwargs):
     x_axis = spectrum.axes_manager.signal_axes[0]
-    ax.plot(x_axis.axis, spectrum.data, color=color, ls=line_style)
+    ax.plot(x_axis.axis, spectrum.data, color=color, ls=linestyle,
+            **kwargs)
     set_xaxis_lims(ax, x_axis)
 
 
@@ -1290,7 +1284,8 @@ def plot_spectra(
         spectra,
         style='overlap',
         color=None,
-        line_style=None,
+        linestyle=None,
+        drawstyle='default',
         padding=1.,
         legend=None,
         legend_picking=True,
@@ -1316,14 +1311,20 @@ def plot_spectra(
         For a list, if its length is less than the number of spectra to plot,
         the colors will be cycled. If `None` (default), use default matplotlib
         color cycle.
-    line_style: None, matplotlib line style, list of line_styles, optional
+    linestyle : {None, matplotlib line style, list of linestyles}, optional
         Sets the line style of the plots (no action on 'heatmap').
-        The main line style are '-','--','steps','-.',':'.
-        For a list, if its length is less than the number of spectra
-        to plot, `line_style` will be cycled, eg. ('-','--','steps','-.',':').
-        If None (default), use continuous lines, eg. '-'.
-    padding : float, optional
-        Option for "cascade". 1.0 (default) guarantees that there is no overlapping.
+        The main line style are ``'-'``, ``'--'``, ``'-.'``, ``':'``.
+        For a list, if its length is less than the number of
+        spectra to plot, linestyle will be cycled.
+        If `None`, use continuous lines (same as ``'-'``).
+    drawstyle : {'default', 'steps', 'steps-pre', 'steps-mid', 'steps-post'},
+        default 'default'
+        The drawstyle determines how the points are connected, no action with
+        ``style='heatmap'``. See
+        :py:meth:`matplotlib.lines.Line2D.set_drawstyle` for more information.
+        The ``'default'`` value is defined by matplotlib.
+    padding : float, optional, default 1.0
+        Option for "cascade". 1 guarantees that there is no overlapping.
         However, in many cases, a value between 0 and 1 can produce a tighter
         plot without overlapping. Negative values have the same effect but
         reverse the order of the spectra without reversing the order of the
@@ -1369,6 +1370,16 @@ def plot_spectra(
 
     """
     import hyperspy.signal
+    if 'line_style' in kwargs.keys():
+        from hyperspy.misc.utils import deprecation_warning
+        deprecation_warning("`line_style` has been renamed to `linestyle` and "
+                            "will be removed in HyperSpy 2.0.")
+        if linestyle is None:
+            linestyle = kwargs.pop('line_style')
+        else:
+            raise ValueError("Both argument `line_style` and `linestyle` have "
+                             "been provided and only one should be used: use "
+                             "`linestyle` only.")
 
     def _reverse_legend(ax_, legend_loc_):
         """
@@ -1405,17 +1416,13 @@ def _reverse_legend(ax_, legend_loc_):
         color = itertools.cycle(
                 plt.rcParams['axes.prop_cycle'].by_key()["color"])
 
-    if line_style is not None:
-        if isinstance(line_style, str):
-            line_style = itertools.cycle([line_style])
-        elif hasattr(line_style, "__iter__"):
-            line_style = itertools.cycle(line_style)
-        else:
-            raise ValueError("line_style must be None, a valid matplotlib "
-                             "line_style string or a list of valid matplotlib "
-                             "line_style.")
+    if linestyle is not None:
+        if isinstance(linestyle, str):
+            linestyle = itertools.cycle([linestyle])
+        elif hasattr(linestyle, "__iter__"):
+            linestyle = itertools.cycle(linestyle)
     else:
-        line_style = ['-'] * len(spectra)
+        linestyle = ['-'] * len(spectra)
 
     if legend is not None:
         if isinstance(legend, str):
@@ -1430,10 +1437,7 @@ def _reverse_legend(ax_, legend_loc_):
             fig = plt.figure(**kwargs)
         if ax is None:
             ax = fig.add_subplot(111)
-        _make_overlap_plot(spectra,
-                           ax,
-                           color=color,
-                           line_style=line_style,)
+        _make_overlap_plot(spectra, ax, color, linestyle, drawstyle=drawstyle)
         if legend is not None:
             ax.legend(legend, loc=legend_loc)
             _reverse_legend(ax, legend_loc)
@@ -1444,25 +1448,26 @@ def _reverse_legend(ax_, legend_loc_):
             fig = plt.figure(**kwargs)
         if ax is None:
             ax = fig.add_subplot(111)
-        _make_cascade_subplot(spectra,
-                              ax,
-                              color=color,
-                              line_style=line_style,
-                              padding=padding)
+        _make_cascade_subplot(spectra, ax, color, linestyle, padding=padding,
+                              drawstyle=drawstyle)
         if legend is not None:
             plt.legend(legend, loc=legend_loc)
             _reverse_legend(ax, legend_loc)
+            if legend_picking is True:
+                animate_legend(fig=fig, ax=ax)
+
     elif style == 'mosaic':
         default_fsize = plt.rcParams["figure.figsize"]
         figsize = (default_fsize[0], default_fsize[1] * len(spectra))
         fig, subplots = plt.subplots(
             len(spectra), 1, figsize=figsize, **kwargs)
         if legend is None:
             legend = [legend] * len(spectra)
-        for spectrum, ax, color, line_style, legend in zip(
-                spectra, subplots, color, line_style, legend):
+        for spectrum, ax, color, linestyle, legend in zip(
+                spectra, subplots, color, linestyle, legend):
             spectrum = _transpose_if_required(spectrum, 1)
-            _plot_spectrum(spectrum, ax, color=color, line_style=line_style)
+            _plot_spectrum(spectrum, ax, color=color, linestyle=linestyle,
+                           drawstyle=drawstyle)
             ax.set_ylabel('Intensity')
             if legend is not None:
                 ax.set_title(legend)
@@ -1575,40 +1580,42 @@ def plot_histograms(signal_list,
                     bins='fd',
                     range_bins=None,
                     color=None,
-                    line_style=None,
+                    linestyle=None,
                     legend='auto',
                     fig=None,
                     **kwargs):
     """Plot the histogram of every signal in the list in one figure.
 
     This function creates a histogram for each signal and plots the list with
-    the `utils.plot.plot_spectra` function.
+    the :py:func:`~.drawing.utils.plot_spectra` function.
 
     Parameters
     ----------
     signal_list : iterable
-        Ordered list of spectra to plot. If `style` is 'cascade' or 'mosaic',
-        the spectra can have different size and axes.
-    bins : int, list, str, optional
+        Ordered list of spectra to plot. If ``style`` is ``"cascade"`` or
+        ``"mosaic"``, the spectra can have different size and axes.
+    bins : {int, list, str}, optional
         If bins is a string, then it must be one of:
-        'knuth' : use Knuth's rule to determine bins,
-        'scott' : use Scott's rule to determine bins,
-        'fd' : use the Freedman-diaconis rule to determine bins (default),
-        'blocks' : use bayesian blocks for dynamic bin widths.
-    range_bins : None, tuple, optional
+
+         - ``'knuth'`` : use Knuth's rule to determine bins,
+         - ``'scott'`` : use Scott's rule to determine bins,
+         - ``'fd'`` : use the Freedman-diaconis rule to determine bins,
+         - ``'blocks'`` : use bayesian blocks for dynamic bin widths.
+    range_bins : {None, tuple}, optional
         The minimum and maximum range for the histogram. If not specified,
-        it will be (x.min(), x.max()). Default None.
-    color : None, valid matplotlib color, list of colors, optional
+        it will be (``x.min()``, ``x.max()``).
+    color : {None, valid matplotlib color, list of colors}, optional
         Sets the color of the lines of the plots. For a list, if its length is
         less than the number of spectra to plot, the colors will be cycled.
-        If None (default), use default matplotlib color cycle.
-    line_style: None, valid matplotlib line style, list of line styles, optional
-        The main line styles are '-','--','steps','-.',':'.
-        For a list, if its length is less than the number of spectra
-        to plot, `line_style` will be cycled, eg. ('-','--','steps','-.',':').
-        If None, use continuous lines.
-    legend: None, list of str, 'auto', optional
-       Display a legend. If 'auto' (default), the title of each spectra
+        If `None`, use default matplotlib color cycle.
+    linestyle: {None, valid matplotlib line style, list of line styles},
+        optional
+        The main line styles are ``'-'``, ``'--'``, ``'-.'``, ``':'``.
+        For a list, if its length is less than the number of
+        spectra to plot, linestyle will be cycled.
+        If `None`, use continuous lines (same as ``'-'``).
+    legend: {None, list of str, 'auto'}, optional
+       Display a legend. If 'auto', the title of each spectra
        (metadata.General.title) is used.
     legend_picking: bool, optional
         If True, a spectrum can be toggled on and off by clicking on
@@ -1625,7 +1632,7 @@ def plot_histograms(signal_list,
 
     >>> img = hs.signals.Signal2D(np.random.chisquare(1,[10,10,100]))
     >>> img2 = hs.signals.Signal2D(np.random.chisquare(2,[10,10,100]))
-    >>> hs.plot.plot_histograms([img,img2],legend=['hist1','hist2'])
+    >>> hs.plot.plot_histograms([img, img2], legend=['hist1', 'hist2'])
 
     Returns
     -------
@@ -1637,10 +1644,9 @@ def plot_histograms(signal_list,
     for obj in signal_list:
         hists.append(obj.get_histogram(bins=bins,
                                        range_bins=range_bins, **kwargs))
-    if line_style is None:
-        line_style = 'steps'
     return plot_spectra(hists, style='overlap', color=color,
-                        line_style=line_style, legend=legend, fig=fig)
+                        linestyle=linestyle, drawstyle='steps-mid',
+                        legend=legend, fig=fig)
 
 
 def picker_kwargs(value, kwargs={}):