What's new
**********

We only cover here the main highlights, for a detailed list of all the changes
see `the github commits changelog
<https://github.com/hyperspy/hyperspy/commits/master>`_.

v0.8.5
======


This is a maintenance release. Follow the following links for details on all
the `bugs fixed
<https://github.com/hyperspy/hyperspy/issues?q=is%3Aissue+milestone%3Anext_maintenance_release+label%3Abug+is%3Aclosed>`_,
`feature <https://github.com/hyperspy/hyperspy/issues?utf8=%E2%9C%93&q=milestone%3Anext_maintenance_release+is%3Aclosed++label%3Aenhancement+>`_
and `documentation
<https://github.com/hyperspy/hyperspy/pulls?utf8=%E2%9C%93&q=milestone%3Anext_maintenance_release+label%3Adocumentation+is%3Aclosed+>`_ enhancements.


It also includes a new feature and introduces an important API change that
will be fully enforced in Hyperspy 1.0.

New feature
-----------

* Widgets to interact with the model components in the Jupyter Notebook.
  See :ref:`here <notebook_interaction-label>` and
  `#1007 <https://github.com/hyperspy/hyperspy/pull/1007>`_ .

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

The new :py:class:`~.signal.BaseSignal`,
:py:class:`~._signals.signal1d.Signal1D` and
:py:class:`~._signals.signal2d.Signal2D` deprecate :py:class:`~.signal.Signal`,
:py:class:`~._signals.spectrum.Spectrum` and :py:class:`~._signals.image.Image`
respectively. Also `as_signal1D`, `as_signal2D`, `to_signal1D` and `to_signal2D`
deprecate `as_spectrum`, `as_image`, `to_spectrum` and `to_image`. See `#963
<https://github.com/hyperspy/hyperspy/pull/963>`_ and `#943
<https://github.com/hyperspy/hyperspy/issues/943>`_ for details.


v0.8.4
======

This release adds support for Python 3 and drops support for Python 2. In all
other respects it is identical to v0.8.3.

v0.8.3
======

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%3Abug&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%3Aenhancement>`_,
`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:

v0.8.2
======

This is a maintenance release that fixes an issue with the Python installers. Those who have successfully installed v0.8.1 do not need to upgrade.

.. _changes_0.8.1:

v0.8.1
======

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%3Abug&utf8=%E2%9C%93>`_,
`feature
<https://github.com/hyperspy/hyperspy/issues?utf8=%E2%9C%93&q=is%3Aclosed+milestone%3A0.8.1++label%3Aenhancement+>`_
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`` :ref:`IPython magic <magic-label>` 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>`.
* :py:meth:`~.signal.Signal.unfolded` context manager.
* :py:meth:`~.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
-----------

* :py:mod:`~.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`` -> ``api.model.components``
    * ``hspy.utils``-> ``api``
    * ``hspy.utils.markers`` ``api.plot.markers``
    * ``hspy.utils.example_signals`` -> ``api.datasets.example_signals``


    In HyperSpy 0.8.1 the full content of :py:mod:`~.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 :py:mod:`~.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 :py:class:`~.signal.Signal` class is now deprecated. We encourage
  all users to use ``isig`` and ``inav`` instead for indexing.
* :py:func:`~.hyperspy.hspy.create_model` is now deprecated in favour of the new
  equivalent :py:meth:`~.signal.Signal.create_model` ``Signal`` method.
* :py:meth:`~.signal.Signal.unfold_if_multidim` is deprecated.


.. _changes_0.8:

v0.8
====

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

Core
^^^^

* :py:meth:`~._signals.spectrum.Spectrum.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 (see
  :ref:`hdf5-format` )


Plotting
^^^^^^^^

* New class,  :py:class:`~.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:`~.drawing.utils.plot_images` function in  ``hspy.utils.plot.plot_images``. See :ref:`plot.images`.
* Improved :py:meth:`~._signals.image.Image.plot` method to customize the image. See :ref:`plot.customize_images`.

EDS
^^^

* New method for quantifying EDS TEM spectra using Cliff-Lorimer method, :py:meth:`~._signals.eds_tem.EDSTEMSpectrum.quantification`. See :ref:`eds_quantification-label`.
* New method to estimate for background subtraction, :py:meth:`~._signals.eds.EDSSpectrum.estimate_background_windows`. See :ref:`eds_background_subtraction-label`.
* New method to estimate the windows of integration, :py:meth:`~._signals.eds.EDSSpectrum.estimate_integration_windows`.
* New specific :py:meth:`~._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 :ref:`eds_plot_markers-label`.
* New examples of signal in the ``hspy.utils.example_signals`` module.

  + :py:func:`~.misc.example_signals_loading.load_1D_EDS_SEM_spectrum`
  + :py:func:`~.misc.example_signals_loading.load_1D_EDS_TEM_spectrum`

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

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

* :py:class:`~.component.Component` and :py:class:`~.component.Parameter` now inherit ``traits.api.HasTraits``
  that enable ``traitsui`` to modify these objects.
* :py:meth:`~.misc.utils.attrsetter` is added, behaving as the default python :py:meth:`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``

v0.7.3
======

This is a maintenance release. A list of fixed issues is available in the
`0.7.3 milestone
<https://github.com/hyperspy/hyperspy/issues?milestone=6&page=1&state=closed>`_
in the github repository.

.. _changes_0.7.2:

v0.7.2
======

This is a maintenance release. A list of fixed issues is available in the
`0.7.2 milestone
<https://github.com/hyperspy/hyperspy/issues?milestone=5&page=1&state=closed>`_
in the github repository.

.. _changes_0.7.1:

v0.7.1
======

This is a maintenance release. A list of fixed issues is available in the
`0.7.1 milestone
<https://github.com/hyperspy/hyperspy/issues?milestone=4&page=1&state=closed>`_
in the github repository.


New features
------------
.. _changes_0.7.1:

* Add suspend/resume model plot updating. See :ref:`model.visualization`.

v0.7
====

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

Core
^^^^

* New syntax to index the :py:class:`~.axes.AxesManager`.
* New Signal methods to transform between Signal subclasses. More information
  :ref:`here <transforming.signal>`.

  + :py:meth:`~.signal.Signal.set_signal_type`
  + :py:meth:`~.signal.Signal.set_signal_origin`
  + :py:meth:`~.signal.Signal.as_image`
  + :py:meth:`~.signal.Signal.as_spectrum`

* The string representation of the Signal class now prints the shape of the
  data and includes a separator between the navigation and the signal axes e.g
  (100, 10| 5) for a signal with two navigation axes of size 100 and 10 and one
  signal axis of size 5.
* Add support for RGBA data. See :ref:`signal.change_dtype`.
* The default toolkit can now be saved in the preferences.
* Added full compatibility with the Qt toolkit that is now the default.
* Added compatibility witn the the GTK and TK toolkits, although with no GUI
  features.
* It is now possible to run HyperSpy in
  :ref:`a headless system <headless-label>`.
* Added a CLI to :py:meth:`~.signal.Signal1DTools.remove_background`.
* New :py:meth:`~.signal.Signal1DTools.estimate_peak_width` method to estimate
  peak width.
* New methods to integrate over one axis:
  :py:meth:`~.signal.Signal.integrate1D` and
  :py:meth:`~.signal.Signal1DTools.integrate_in_range`.
* New :attr:`~signal.Signal.metadata` attribute, ``Signal.binned``. Several
  methods behave differently on binned and unbinned signals.
  See :ref:`signal.binned`.
* New :py:meth:`~.signal.Signal.map` method to easily transform the
  data using a function that operates on individual signals. See
  :ref:`signal.iterator`.
* New :py:meth:`~.signal.Signal.get_histogram` and
  :py:meth:`~.signal.Signal.print_summary_statistics` methods.
* The spikes removal tool has been moved to the :class:`~._signal.Spectrum`
  class so that it is available for all its subclasses.
* The :py:meth:`~.signal.Signal.split` method now can automatically split back
  stacked signals into its original part. See :ref:`signal.stack_split`.

IO
^^

* Improved support for FEI's emi and ser files.
* Improved support for Gatan's dm3 files.
* Add support for reading Gatan's dm4 files.

Plotting
^^^^^^^^

* Use the blitting capabilities of the different toolkits to
  speed up the plotting of images.
* Added several extra options to the Signal :py:meth:`~.signal.Signal.plot`
  method to customize the navigator. See :ref:`visualization-label`.
* Add compatibility with IPython's matplotlib inline plotting. See
  :ref:`inline_plotting`.
* New function, :py:func:`~.drawing.utils.plot_spectra`, to plot several
  spectra in the same figure. See :ref:`plot.spectra`.
* New function, :py:func:`~.drawing.utils.plot_signals`, to plot several
  signals at the same time. See :ref:`plot.signals`.
* New function, :py:func:`~.drawing.utils.plot_histograms`, to plot the histrograms
  of several signals at the same time. See :ref:`plot.signals`.

Curve fitting
^^^^^^^^^^^^^

* The chi-squared, reduced chi-squared and the degrees of freedom are
  computed automatically when fitting. See :ref:`model.fitting`.
* New functionality to plot the individual components of a model. See
  :ref:`model.visualization`.
* New method, :py:meth:`~.model.Model.fit_component`, to help setting the
  starting parameters. See :ref:`model.starting`.

Machine learning
^^^^^^^^^^^^^^^^

* The PCA scree plot can now be easily obtained as a Signal. See
  :ref:`scree-plot`.
* The decomposition and blind source separation components can now be obtained
  as :py:class:`~.signal.Signal` instances. See :ref:`mva.get_results`.
* New methods to plot the decomposition and blind source separation results
  that support n-dimensional loadings. See :ref:`mva.visualization`.

Dielectric function
^^^^^^^^^^^^^^^^^^^

* New :class:`~.signal.Signal` subclass,
  :class:`~._signals.dielectric_function.DielectricFunction`.

EELS
^^^^

* New method,
  :meth:`~._signals.eels.EELSSpectrum.kramers_kronig_analysis` to calculate
  the dielectric function from low-loss electron energy-loss spectra based on
  the Kramers-Kronig relations. See :ref:`eels.kk`.
* New method to align the zero-loss peak,
  :meth:`~._signals.eels.EELSSpectrum.align_zero_loss_peak`.

EDS
^^^

* New signal, EDSSpectrum especialized in EDS data analysis, with subsignal
  for EDS with SEM and with TEM: EDSSEMSpectrum and EDSTEMSpectrum. See
  :ref:`eds-label`.
* New database of EDS lines available in the ``elements`` attribute of the
  ``hspy.utils.material`` module.
* Adapted methods to calibrate the spectrum, the detector and the microscope.
  See :ref:`eds_calibration-label`.
* Specific methods to describe the sample,
  :py:meth:`~._signals.eds.EDSSpectrum.add_elements` and
  :py:meth:`~._signals.eds.EDSSpectrum.add_lines`. See :ref:`eds_sample-label`
* New method to get the intensity of specific X-ray lines:
  :py:meth:`~._signals.eds.EDSSpectrum.get_lines_intensity`. See
  :ref:`eds_plot-label`

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

* hyperspy.misc has been reorganized. Most of the functions in misc.utils has
  been rellocated to specialized modules. misc.utils is no longer imported in
  hyperspy.hspy. A new hyperspy.utils module is imported instead.
* Objects that have been renamed

  + ``hspy.elements`` -> ``utils.material.elements``.
  + ``Signal.navigation_indexer`` -> ``inav``.
  + ``Signal.signal_indexer`` -> ``isig``.
  + ``Signal.mapped_parameters`` -> ``Signal.metadata``.
  + ``Signal.original_parameters`` -> ``Signal.original_metadata``.
* The metadata has been reorganized. See :ref:`metadata_structure`.
* The following signal methods now operate out-of-place:

  + :py:meth:`~.signal.Signal.swap_axes`
  + :py:meth:`~.signal.Signal.rebin`

.. _changes_0.6:

v0.6
====

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

* Signal now supports indexing and slicing. See :ref:`signal.indexing`.
* Most arithmetic and rich arithmetic operators work with signal.
  See :ref:`signal.operations`.
* Much improved EELSSpectrum methods:
  :py:meth:`~._signals.eels.EELSSpectrum.estimate_zero_loss_peak_centre`,
  :py:meth:`~._signals.eels.EELSSpectrum.estimate_elastic_scattering_intensity` and
  :py:meth:`~._signals.eels.EELSSpectrum.estimate_elastic_scattering_threshold`.

* The axes can now be given using their name e.g. ``s.crop("x", 1,10)``
* New syntax to specify position over axes: an integer specifies the indexes
  over the axis and a floating number specifies the position in the axis units
  e.g. ``s.crop("x", 1, 10.)`` crops over the axis `x` (in meters) from index 1
  to value 10 meters. Note that this may make your old scripts behave in
  unexpected ways as just renaming the old \*_in_units and \*_in_values methods
  won't work in most cases.
* Most methods now use the natural order i.e. X,Y,Z.. to index the axes.
* Add padding to fourier-log and fourier-ratio deconvolution to fix the
  wrap-around problem and increase its performance.
* New
  :py:meth:`~.components.eels_cl_edge.EELSCLEdge.get_fine_structure_as_spectrum`
  EELSCLEdge method.
* New :py:class:`~.components.arctan.Arctan` model component.
* New
  :py:meth:`~.model.Model.enable_adjust_position`
  and :py:meth:`~.model.Model.disable_adjust_position`
  to easily change the position of components using the mouse on the plot.
* New Model methods
  :py:meth:`~.model.Model.set_parameters_value`,
  :py:meth:`~.model.Model.set_parameters_free` and
  :py:meth:`~.model.Model.set_parameters_not_free`
  to easily set several important component attributes of a list of components
  at once.
* New
  :py:func:`~.misc.utils.stack` function to stack signals.
* New Signal methods:
  :py:meth:`~.signal.Signal.integrate_simpson`,
  :py:meth:`~.signal.Signal.max`,
  :py:meth:`~.signal.Signal.min`,
  :py:meth:`~.signal.Signal.var`, and
  :py:meth:`~.signal.Signal.std`.
* New sliders window to easily navigate signals with navigation_dimension > 2.
* The Ripple (rpl) reader can now read rpl files produced by INCA.

API changes
-----------
* The following functions has been renamed or removed:

    * components.EELSCLEdge

        * knots_factor -> fine_structure_smoothing
        * edge_position -> onset_energy
        * energy_shift removed

    * components.Voigt.origin -> centre
    * signals.Spectrum

        * find_peaks_1D -> Signal.find_peaks1D_ohaver
        * align_1D -> Signal.align1D
        * shift_1D -> Signal.shift1D
        * interpolate_1D -> Signal.interpolate1D

    * signals.Image.estimate_2D_translation -> Signal.estimate_shift2D
    * Signal

        * split_in -> split
        * crop_in_units -> crop
        * crop_in_pixels -> crop


* Change syntax to create Signal objects. Instead of a dictionary
  Signal.__init__ takes keywords e.g with  a new syntax .
  ``>>> s = signals.Signal1D(np.arange(10))`` instead of
  ``>>> s = signals.Signal1D({'data' : np.arange(10)})``



.. _changes_0.5.1:

v0.5.1
======

New features
------------
* New Signal method `get_current_signal` proposed by magnunor.
* New Signal `save` method keyword `extension` to easily change the saving format while keeping the same file name.
* New EELSSpectrum methods: estimate_elastic_scattering_intensity, fourier_ratio_deconvolution, richardson_lucy_deconvolution, power_law_extrapolation.
* New Spectrum method: hanning_taper.



Major bugs fixed
----------------
* The `print_current_values` Model method was raising errors when fine structure was enabled or when only_free = False.
*  The `load` function `signal_type` keyword was not passed to the readers.
* The spikes removal tool was unable to find the next spikes when the spike was detected close to the limits of the spectrum.
* `load` was raising an UnicodeError when the title contained non-ASCII characters.
* In Windows `HyperSpy Here` was opening in the current folder, not in the selected folder.
* The fine structure coefficients were overwritten with their std when charging values from the model.
* Storing the parameters in the maps and all the related functionality was broken for 1D spectrum.
* Remove_background was broken for 1D spectrum.




API changes
-----------
* EELSSPectrum.find_low_loss_centre was renamed to estimate_zero_loss_peak_centre.
* EELSSPectrum.calculate_FWHM was renamed to estimate_FWHM.

.. _changes_0.5:

v0.5
====

New features
------------
* The documentation was thoroughly revised, courtesy of M. Walls.
* New user interface to remove spikes from EELS spectra.
* New align2D signals.Image method to align image stacks.
* When loading image files, the data are now automatically converted to
  grayscale when all the color channels are equal.
* Add the possibility to load a stack memory mapped (similar to ImageJ
  virtual stack).
* Improved hyperspy starter script that now includes the possibility
  to start HyperSpy in the new IPython notebook.
* Add "HyperSpy notebook here" to the Windows context menu.
* The information displayed in the plots produced by Signal.plot have
  been enhanced.
* Added Egerton's sigmak3 and sigmal3 GOS calculations (translated
  from matlab by I. Iyengar) to the EELS core loss component.
* A browsable dictionary containing the chemical elements and
  their onset energies is now available in the user namespace under
  the variable name `elements`.
* The ripple file format now supports storing the beam energy, the collection and the convergence angle.


Major bugs fixed
----------------
* The EELS core loss component had a bug in the calculation of the
  relativistic gamma that produced a gamma that was always
  approximately zero. As a consequence the GOS calculation was wrong,
  especially for high beam energies.
* Loading msa files was broken when running on Python 2.7.2 and newer.
* Saving images to rpl format was broken.
* Performing BSS on data decomposed with poissonian noise normalization
  was failing when some columns or rows of the unfolded data were zero,
  what occurs often in EDX data for example.
* Importing some versions of scikits learn was broken
* The progress bar was not working properly in the new IPython notebook.
* The constrast of the image was not automatically updated.

API changes
-----------
* spatial_mask was renamed to navigation_mask.
* Spectrum and Image are not loaded into the user namespace by default.
  The signals module is loaded instead.
* Change the default BSS algorithm to sklearn fastica, that is now
  distributed with HyperSpy and used in case that sklearn is not
  installed e.g. when using EPDFree.
* _slicing_axes was renamed to signal_axes.
* _non_slicing_axes to navigation_axes.
* All the Model \*_in_pixels methods  were renamed to to _*_in_pixel.
* EELSCLEdge.fs_state was renamed to fine_structure_active.
* EELSCLEdge.fslist was renamed to fine_structure_coeff.
* EELSCLEdge.fs_emax was renamed to fine_structure_width.
* EELSCLEdge.freedelta was renamed to free_energy_shift.
* EELSCLEdge.delta was renamed to energy_shift.
* A value of True in a mask now means that the item is masked all over
  HyperSpy.


.. _changes_0.4.1:

v0.4.1
======

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

 * Added TIFF 16, 32 and 64 bits support by using (and distributing) Christoph Gohlke's `tifffile library <http://www.lfd.uci.edu/~gohlke/code/tifffile.py.html>`_.
 * Improved UTF8 support.
 * Reduce the number of required libraries by making mdp and hdf5 not mandatory.
 * Improve the information returned by __repr__ of several objects.
 * DictionaryBrowser now has an export method, i.e. mapped parameters and original_parameters can be exported.
 * New _id_name attribute for Components and Parameters. Improvements in their __repr__ methods.
 * Component.name can now be overwriten by the user.
 * New Signal.__str__ method.
 * Include HyperSpy in The Python Package Index.


Bugs fixed
----------
 * Non-ascii characters breaking IO and print features fixed.
 * Loading of multiple files at once using wildcards fixed.
 * Remove broken hyperspy-gui script.
 * Remove unmantained and broken 2D peak finding and analysis features.

Syntax changes
--------------
 * In EELS automatic background feature creates a PowerLaw component, adds it to the model an add it to a variable in the user namespace. The variable has been renamed from `bg` to `background`.
 * pes_gaussian Component renamed to pes_core_line_shape.

.. _changes_0.4:

v0.4
====

New features
------------
 * Add a slider to the filter ui.
 * Add auto_replot to sum.
 * Add butterworth filter.
 * Added centring and auto_transpose to the svd_pca algorithm.
 * Keep the mva_results information when changing the signal type.
 * Added sparse_pca and mini_batch_sparse_pca to decomposition algorithms.
 * Added TV to the smoothing algorithms available in BSS.
 * Added whitening to the mdp ICA preprocessing.
 * Add explained_variance_ratio.
 * Improvements in saving/loading mva data.
 * Add option to perform ICA on the scores.
 * Add orthomax FA algorithm.
 * Add plot methods to Component and Parameter.
 * Add plot_results to Model.
 * Add possibility to export the decomposition and bss results to a folder.
 * Add Signal method `change_dtype`.
 * Add the possibility to pass extra parameters to the ICA algorithm.
 * Add the possibility to reproject the data after a decomposition.
 * Add warning when decomposing a non-float signal.
 * adds a method to get the PCs as a Spectrum object and adds smoothing to the ICA preprocessing.
 * Add the possibility to select the energy range in which to perform spike removal operations.
 * the smoothings guis now offer differentiation and line color option. Smoothing now does not require a gui.
 * Fix reverse_ic which was not reversing the scores and improve the autoreversing method.
 * Avoid cropping when is not needed.
 * Changed criteria to reverse the ICs.
 * Changed nonans default to False for plotting.
 * Change the whitening algorithm to a svd based one and add sklearn fastica algorithm.
 * Clean the ummixing info after a new decomposition.
 * Increase the chances that similar independent components will have the same indexes.
 * Make savitzky-golay smoothing work without raising figures.
 * Make plot_decomposition* plot only the number of factors/scores determined by output_dimension.
 * make the Parameter __repr__ method print its name.
 * New contrast adjustment tool.
 * New export method for Model, Component and Parameter.
 * New Model method: print_current_values.
 * New signal, spectrum_simulation.
 * New smoothing algorithm: total variance denoising.
 * Plotting the components in the same or separate windows is now configurable in the preferences.
 * Plotting the spikes is now optional.
 * Return an error message when the decomposition algorithm is not recognised.
 * Store the masks in mva_results.
 * The free parameters are now automically updated on chaning the free attribute.

Bugs fixed
----------
 * Added missing keywords to plot_pca_factors and plot_ica_factors.
 * renamed incorrectly named exportPca and exportIca functions.
 * an error was raised when calling generate_data_from_model.
 * a signal with containing nans was failing to plot.
 * attempting to use any decomposition plotting method after loading with mva_results.load was raising an error.
 * a typo was causing in error in pca when normalize_variance = True.
 * a typo was raising an error when cropping the decomposition dimension.
 * commit 5ff3798105d6 made decomposition and other methods raise an error.
 * BUG-FIXED: the decomposition centering index was wrong.
 * ensure_directory was failing for the current directory.
 * model data forced to be 3D unnecessarily.
 * non declared variable was raising an error.
 * plot naming for peak char factor plots were messed up.
 * plot_RGB was broken.
 * plot_scores_2D was using the transpose of the shape to reshape the scores.
 * remove background was raising an error when the navigation dimension was 0.
 * saving the scores was sometimes transposing the shape.
 * selecting indexes while using the learning export functions was raising an error.
 * the calibrate ui was calculating wrongly the calibration the first time that Apply was pressed.
 * the offset estimation was summing instead of averaging.
 * the plot_explained_variance_ratio was actually plotting the cumulative, renamed.
 * the signal mask in decomposition and ica was not being raveled.
 * the slice attribute was not correctly set at init in some scenarios.
 * the smoothing and calibrabrion UIs were freezing when the plots where closed before closing the UI window.
 * to_spectrum was transposing the navigation dimension.
 * variance2one was operating in the wrong axis.
 * when closing the plots of a model, the UI object was not being destroyed.
 * when plotting an image the title was not displayed.
 * when the axis size was changed (e.g. after cropping) the set_signal_dimension method was not being called.
 * when using transform the data was being centered and the resulting scores were wrong.

Syntax changes
--------------

 * in decomposition V rename to explained_variance.
 * In FixedPattern, default interpolation changed to linear.
 * Line and parabole components deleted + improvements in the docstrings.
 * pca_V = variance.
 * mva_result renamed to learning_results.
 * pca renamed to decomposition.
 * pca_v and mva_results.v renamed to scores pc renamed to factors .
   pca_build_SI renamed to get_pca_model ica_build_SI renamed to get_ica_model.
 * plot_explained_variance renamed to plot_explained_variance_ratio.
 * principal_components_analysis renamed to decomposition.
 * rename eels_simulation to eels_spectrum_simulation.
 * Rename the output parameter of svd_pca and add scores.
 * Replace plot_lev by plot_explained_variance_ratio.
 * Scores renamed to loadings.
 * slice_bool renamed to navigate to make its function more explicit.
 * smoothing renamed to pretreatment and butter added.
 * variance2one renamed to normalize_variance.
 * w renamed to unmixing matrix and fixes a bug when loading a mva_result
   in which output_dimension = None.
 * ubshells are again availabe in the interactive session.
 * Several changes to the interface.
 * The documentation was updated to reflex the last changes.
 * The microscopes.csv file was updated so it no longer contains the
   Orsay VG parameters.
