hyperspy · ericpre · Jan 21, 2023 · Jan 20, 2023
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,3 +1,5 @@
+.. _changelog:
+
 Changelog
 *********
 

diff --git a/doc/user_guide/axes.rst b/doc/user_guide/axes.rst
@@ -1,6 +1,9 @@
+.. _axes-handling:
+
 Axes handling
 *************
 
+.. _dimensions-label:
 
 The navigation and signal dimensions
 ------------------------------------
@@ -164,6 +167,7 @@ navigation dimensions:
 
     >>> s.axes_manager.indices = (5, 4)
 
+.. _Axes_properties:
 
 Summary of axis properties
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -237,6 +241,8 @@ following table.
     will be added in future releases.
 
 
+.. _uniform-data-axis:
+
 Uniform data axis
 ^^^^^^^^^^^^^^^^^
 
@@ -274,6 +280,8 @@ Corresponding output of :py:class:`~.axes.AxesManager`:
                      |    500 |     300 |       1 |
 
 
+.. _functional-data-axis:
+
 Functional data axis
 ^^^^^^^^^^^^^^^^^^^^
 
@@ -362,6 +370,8 @@ Initializing ``x`` as non-uniform :py:class:`~.axes.DataAxis`:
 Initializing ``x`` with ``offset`` and ``scale``:
 
 
+.. _data-axis:
+
 (non-uniform) Data axis
 ^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -395,6 +405,8 @@ Corresponding output of :py:class:`~.axes.AxesManager`:
                      |     12 | non-uniform axis | non-uniform axis |
 
 
+.. _defining-axes:
+
 Defining a new axis
 -------------------
 

diff --git a/doc/user_guide/basic_usage.rst b/doc/user_guide/basic_usage.rst
@@ -1,3 +1,5 @@
+.. _basic-usage:
+
 Basic Usage
 ===========
 

diff --git a/doc/user_guide/bibliography.rst b/doc/user_guide/bibliography.rst
@@ -1,5 +1,7 @@
 :html_theme.sidebar_secondary.remove: true
 
+.. _bibliography:
+
 Bibliography
 ============
 

diff --git a/doc/user_guide/dielectric_function.rst b/doc/user_guide/dielectric_function.rst
@@ -1,3 +1,6 @@
+
+.. _dielectric-function-label:
+
 Dielectric function tools
 -------------------------
 

diff --git a/doc/user_guide/eels.rst b/doc/user_guide/eels.rst
@@ -1,3 +1,4 @@
+.. _eels-label:
 
 Electron Energy Loss Spectroscopy
 *********************************

diff --git a/doc/user_guide/model/adding_components.rst b/doc/user_guide/model/adding_components.rst
@@ -1,3 +1,5 @@
+.. _adding-components:
+
 Adding components to the model
 ------------------------------
 

diff --git a/doc/user_guide/model/creating_model.rst b/doc/user_guide/model/creating_model.rst
@@ -1,3 +1,4 @@
+.. _creating_model:
 
 Creating a model
 ----------------

diff --git a/doc/user_guide/model/model_components.rst b/doc/user_guide/model/model_components.rst
@@ -1,3 +1,5 @@
+.. _model-components:
+
 Model components
 ----------------
 

diff --git a/doc/user_guide/model/model_parameters.rst b/doc/user_guide/model/model_parameters.rst
@@ -1,3 +1,5 @@
+.. _model-intro:
+
 Getting and setting parameter values and attributes
 ---------------------------------------------------
 

diff --git a/doc/user_guide/mva/export_results.rst b/doc/user_guide/mva/export_results.rst
@@ -1,3 +1,5 @@
+.. _mva.export:
+
 Export results
 ==============
 

diff --git a/doc/user_guide/signal/basic_statistical_analysis.rst b/doc/user_guide/signal/basic_statistical_analysis.rst
@@ -1,3 +1,5 @@
+.. _signal.statistics:
+
 Basic statistical analysis
 --------------------------
 

diff --git a/doc/user_guide/signal/generic_tools.rst b/doc/user_guide/signal/generic_tools.rst
@@ -6,8 +6,9 @@ more details about a particular method click on its name. For a detailed list
 of all the methods available see the :py:class:`~.api.signals.BaseSignal` documentation.
 
 The methods of this section are available to all the signals. In other chapters
-methods that are only available in specialized
-subclasses.
+methods that are only available in specialized subclasses are listed.
+
+.. _math.operations:
 
 Mathematical operations
 ^^^^^^^^^^^^^^^^^^^^^^^

diff --git a/doc/user_guide/signal/index.rst b/doc/user_guide/signal/index.rst
@@ -1,3 +1,5 @@
+.. _signal-label:
+
 The Signal class
 ****************
 

diff --git a/doc/user_guide/signal1d.rst b/doc/user_guide/signal1d.rst
@@ -1,10 +1,12 @@
+.. _signal1D-label:
 
 Signal1D Tools
 **************
 
 The methods described in this section are only available for one-dimensional
 signals in the Signal1D class.
 
+
 .. _signal1D.crop:
 
 Cropping
@@ -44,6 +46,7 @@ It is possible to crop interactively using :ref:`roi-label`. For example:
 
    Interactive spectrum cropping using a ROI.
 
+
 .. _signal1D.remove_background:
 
 Background removal
@@ -80,12 +83,14 @@ Example of usage:
    figure) click inside the axes of the figure and drag to the right
    without releasing the button.
 
+
 Calibration
 -----------
 
 The :py:meth:`~._signals.signal1d.Signal1D.calibrate` method provides a user
 interface to calibrate the spectral axis.
 
+
 Alignment
 ---------
 
@@ -96,16 +101,20 @@ files.
 * :py:meth:`~._signals.signal1d.Signal1D.align1D`
 * :py:meth:`~._signals.signal1d.Signal1D.shift1D`
 
+
 .. _integrate_1D-label:
 
 Integration
 -----------
 
-.. deprecated:: 1.3
-    :py:meth:`~._signals.signal1d.Signal1D.integrate_in_range`.
-    It will be removed in 2.0. Use :py:meth:`~.signal.BaseSignal.integrate1D`
-    instead, possibly in combination with a :ref:`ROI-label` if interactivity
-    is required.
+To integrate signals use the :py:meth:`~.signal.BaseSignal.integrate1D` method.
+Possibly in combination with a :ref:`ROI-label` if interactivity is required.
+Otherwise, a signal subrange for integration can also be chosen with the
+:py:attr:`~.api.signals.BaseSignal.isig` method.
+
+.. code-block:: python
+
+    >>> s.isig[0.2:0.5].integrate1D(axis=0)
 
 
 Data smoothing
@@ -119,6 +128,7 @@ passed) can perform data smoothing with different algorithms:
 * :py:meth:`~._signals.signal1d.Signal1D.smooth_tv`
 * :py:meth:`~._signals.signal1d.Signal1D.smooth_savitzky_golay`
 
+
 Spike removal
 --------------
 
@@ -160,6 +170,15 @@ through the :py:meth:`~._signals.signal1d.Signal1D.find_peaks1D_ohaver`
 method.
 
 
+Estimate peak width
+-------------------
+
+For asymmetric peaks, `fitted functions <model.fitting>` may not provide
+an accurate description of the peak, in particular the peak width. The function
+:py:meth:`~._signals.signal1d.Signal1D.estimate_peak_width`
+determines the width of a peak at a certain fraction of its maximum value.
+
+
 Other methods
 -------------
 

diff --git a/doc/user_guide/signal2d.rst b/doc/user_guide/signal2d.rst
@@ -1,4 +1,6 @@
 
+.. _signal2d-label:
+
 Signal2D Tools
 **************