diff --git a/doc/source/user_guide/fitting_luminescence.rst b/doc/source/user_guide/fitting_luminescence.rst index b43610cd3..dd62296e4 100644 --- a/doc/source/user_guide/fitting_luminescence.rst +++ b/doc/source/user_guide/fitting_luminescence.rst @@ -3,12 +3,17 @@ Fitting luminescence data ************************* -LumiSpy is compatible with :external+hyperspy:ref:`HyperSpy model fitting +LumiSpy is compatible with :external+hyperspy:doc:`HyperSpy model fitting `. -It can fit using both `uniform and and non-uniform axes -`_ +It can fit using both :external+hyperspy:ref:`uniform and and non-uniform axes +` (e.g. energy scale). A general introduction can be found in the -:external+hyperspy:ref:`HyperSpy user guide `. +:external+hyperspy:doc:`HyperSpy user guide `. + +A detailed example is given in the ``Fitting_tutorial`` in the +`HyperSpy demos repository `_. +See also the `LumiSpy demo notebooks `_ +for examples of data fitting. .. Note:: The :ref:`jacobian` may affect the shape, in particular of broader peaks. @@ -19,8 +24,7 @@ It can fit using both `uniform and and non-uniform axes TODO: Show how to extract the *modeled signal* with all/one component. -See also the `LumiSpy demo notebooks `_ -for examples of data fitting. + .. _fitting_variance: @@ -31,4 +35,4 @@ TODO: Documentation on variance handling in the context of fitting, in particular using :external:py:meth:`estimate_poissonian_noise_variance() ` -See [Tappy]_ +For a detailed discussion, see [Tappy]_ diff --git a/doc/source/user_guide/introduction.rst b/doc/source/user_guide/introduction.rst index a3bafca70..60a20e9a4 100644 --- a/doc/source/user_guide/introduction.rst +++ b/doc/source/user_guide/introduction.rst @@ -26,11 +26,11 @@ that can be described as multidimensional arrays of a given signal. Notable features that **HyperSpy** provides are: -- :external+hyperspy:ref:`base signal classes ` +- :external+hyperspy:doc:`base signal classes ` for the handling of (multidimensional) spectral data, - the necessary tools for loading :external+hyperspy:ref:`various data file formats `, -- :external+hyperspy:ref:`analytical tools ` +- :external+hyperspy:doc:`analytical tools ` that exploit the multidimensionality of datasets, - a user-friendly and powerful framework for :external+hyperspy:ref:`model fitting ` that @@ -137,7 +137,7 @@ but also bug reports and feature requests from any other users. Don't hesitate to join the discussions! Currrently, we have implemented the base functionality that extends -`HyperSpy's capabilities `_ +:external+hyperspy:ref:`HyperSpy's capabilities ` to additional signal classes. In the near future, the following functions should be developed: diff --git a/doc/source/user_guide/metadata_structure.rst b/doc/source/user_guide/metadata_structure.rst index fabbf55a1..92e05a2db 100644 --- a/doc/source/user_guide/metadata_structure.rst +++ b/doc/source/user_guide/metadata_structure.rst @@ -6,7 +6,7 @@ LumiSpy metadata structure LumiSpy extends the :external+hyperspy:ref:`HyperSpy metadata structure ` with conventions for metadata specific to its signal types. Refer to the -:external+hyperspy:ref:`HyperSpy metadata documentation ` +:external+hyperspy:doc:`HyperSpy metadata documentation ` for general metadata fields. The metadata of any **signal objects** is stored in the `metadata` attribute, diff --git a/doc/source/user_guide/signal_tools.rst b/doc/source/user_guide/signal_tools.rst index a70d94de6..b63b83f35 100644 --- a/doc/source/user_guide/signal_tools.rst +++ b/doc/source/user_guide/signal_tools.rst @@ -123,7 +123,7 @@ This function also works for non-linear axes. For the based on the function used to create the non-uniform axis. For :external:py:class:`hyperspy.axes.DataAxis`, a linear interpolation between the axes points at the center of mass is assumed, but this behaviour can be changed -with the `kwargs` of :external:py:meth:`scipy.interpolate.interp1d` function. +with the `kwargs` of :external:py:class:`scipy.interpolate.interp1d` function. .. code-block:: python diff --git a/lumispy/signals/cl_spectrum.py b/lumispy/signals/cl_spectrum.py index dee373d59..b5944ad20 100644 --- a/lumispy/signals/cl_spectrum.py +++ b/lumispy/signals/cl_spectrum.py @@ -79,7 +79,6 @@ def remove_spikes( interactive=False, **kwargs ): - if luminescence_roi is not None and signal_mask is not None: raise AttributeError( "Only either `luminescence_roi` or the `signal_mask` can be an input."