Hyperspy

===================

This is a maintenance release that includes fixes for multiple bugs, some
enhancements, new features and API changes. This is set to be the last HyperSpy
release for Python 2. The release (HyperSpy 0.8.4) will support only Python 3.

Importantly, the way to start HyperSpy changes (again) in this release. Please
read carefully :ref:`importing_hyperspy-label` for details.

The broadcasting rules have also changed. See :ref:`signal.operations`
for details.

Follow the following links for details on all the `bugs fixed
<https://github.com/hyperspy/hyperspy/issues?page=1&q=is%3Aclosed+milestone%3A0.8.3+label%3A"type%3A+bug"&utf8=%E2%9C%93>`__,
`documentation enhancements
<https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3A0.8.3+label%3Adocumentation>`__,
`enhancements
<https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3A0.8.3+label%3A"type%3A+enhancement">`__,
`new features
<https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3A0.8.3+label%3ANew>`__
`and API changes
<https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3A0.8.3+label%3A"Api+change">`__


.. _changes_0.8.2:

===================

This is a maintenance release that fixes an issue with the Python installers. Those who have successfully installed 0.8.1 do not need to upgrade.

.. _changes_0.8.1:

===================

This is a maintenance release. Follow the following links for details on all
the `bugs fixed
<https://github.com/hyperspy/hyperspy/issues?page=1&q=is%3Aclosed+milestone%3A0.8.1+label%3A"type%3A+bug"&utf8=%E2%9C%93>`__,
`feature
<https://github.com/hyperspy/hyperspy/issues?utf8=%E2%9C%93&q=is%3Aclosed+milestone%3A0.8.1++label%3A"type%3A+enhancement"+>`__
and `documentation
<https://github.com/hyperspy/hyperspy/issues?q=is%3Aclosed+milestone%3A0.8.1+label%3Adocumentation>`__ enhancements.

Importantly, the way to start HyperSpy changes in this release. Read :ref:`importing_hyperspy-label` for details.

It also includes some new features and introduces important API changes that
will be fully enforced in Hyperspy 1.0.

New features
------------
* Support for IPython 3.0.
* ``%hyperspy`` IPython magic to easily and transparently import HyperSpy, matplotlib and numpy when using IPython.
* :py:class:`~._components.expression.Expression` model component to easily create analytical function components. More details
:ref:`here <expression_component-label>`.
* ``hyperspy.signal.Signal.unfolded`` context manager.
* ``hyperspy.signal.Signal.derivative`` method.
* :ref:`syntax to access the components in the model <model_components-label>`
that includes pretty printing of the components.

API changes
-----------

* ``hyperspy.hspy`` is now deprecated in favour of the new
:py:mod:`hyperspy.api`. The new API renames and/or move several modules as
folows:

* ``hspy.components`` -> ``hyperspy.api.model.components``
* ``hspy.utils``-> ``hyperspy.api``
* ``hspy.utils.markers`` ``hyperspy.api.plot.markers``
* ``hspy.utils.example_signals`` -> ``hyperspy.api.datasets.example_signals``


In HyperSpy 0.8.1 the full content of ``hyperspy.hspy`` is still
imported in the user namespace, but this can now be disabled in
``hs.preferences.General.import_hspy``. In Hyperspy 1.0 it will be
disabled by default and the ``hyperspy.hspy`` module will be fully
removed in HyperSpy 0.10. We encourage all users to migrate to the new
syntax. For more details see :ref:`importing_hyperspy-label`.
* Indexing the ``hyperspy.signal.Signal`` class is now deprecated. We encourage
all users to use ``isig`` and ``inav`` instead for indexing.
* ``hyperspy.hspy.create_model`` is now deprecated in favour of the new
equivalent ``hyperspy.signal.Signal.create_model`` ``Signal`` method.
* ``hyperspy.signal.Signal.unfold_if_multidim`` is deprecated.


.. _changes_0.8:

===================

New features
------------

Core
^^^^

* :py:meth:`~.api.signals.Signal1D.spikes_removal_tool` displays derivative max value when used with
GUI.
* Progress-bar can now be suppressed by passing ``show_progressbar`` argument to all functions that generate
it.

IO
^^

* HDF5 file format now supports saving lists, tuples, binary strings and signals in metadata.


Plotting
^^^^^^^^

* New class, ``hyperspy.drawing.marker.MarkerBase``, to plot markers with ``hspy.utils.plot.markers`` module. See :ref:`plot.markers`.
* New method to plot images with the :py:func:`~.api.plot.plot_images` function in ``hspy.utils.plot.plot_images``. See :ref:`plot.images`.
* Improved ``hyperspy._signals.image.Signal2D.plot`` method to customize the image. See :ref:`plot.customize_images`.

EDS
^^^

* New method for quantifying EDS TEM spectra using Cliff-Lorimer method, ``hyperspy._signals.eds_tem.EDSTEMSpectrum.quantification``. See :external+exspy:ref:`eds_quantification-label`.
* New method to estimate for background subtraction, ``hyperspy._signals.eds.EDSSpectrum.estimate_background_windows``. See :external+exspy:ref:`eds_background_subtraction-label`.
* New method to estimate the windows of integration, ``hyperspy._signals.eds.EDSSpectrum.estimate_integration_windows``.
* New specific ``hyperspy._signals.eds.EDSSpectrum.plot`` method, with markers to indicate the X-ray lines, the window of integration or/and the windows for background subtraction. See :external+exspy:ref:`eds_plot_markers-label`.
* New examples of signal in the ``hspy.utils.example_signals`` module.

+ ``hyperspy.misc.example_signals_loading.load_1D_EDS_SEM_spectrum``
+ ``hyperspy.misc.example_signals_loading.load_1D_EDS_TEM_spectrum``

* New method to mask the vaccum, ``hyperspy._signals.eds_tem.EDSTEMSpectrum.vacuum_mask`` and a specific ``hyperspy._signals.eds_tem.EDSTEMSpectrum.decomposition`` method that incoroporate the vacuum mask

API changes
-----------

* :py:class:`~hyperspy.component.Component` and :py:class:`~hyperspy.component.Parameter` now inherit ``traits.api.HasTraits``
that enable ``traitsui`` to modify these objects.
* ``hyperspy.misc.utils.attrsetter`` is added, behaving as the default python ``setattr`` with nested
attributes.
* Several widget functions were made internal and/or renamed:
+ ``add_patch_to`` -> ``_add_patch_to``
+ ``set_patch`` -> ``_set_patch``
+ ``onmove`` -> ``_onmousemove``
+ ``update_patch_position`` -> ``_update_patch_position``
+ ``update_patch_size`` -> ``_update_patch_size``
+ ``add_axes`` -> ``set_mpl_ax``

<https://github.com/hyperspy/hyperspy/issues?milestone=6&page=1&state=closed>`__
in the github repository.

.. _changes_0.7.2:

<https://github.com/hyperspy/hyperspy/issues?milestone=5&page=1&state=closed>`__
in the github repository.

.. _changes_0.7.1: