Hyperspy

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

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 Signal1D 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:

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

New features
------------
* The documentation was thoroughly revised, courtesy of M. Walls.
* New user interface to remove spikes from EELS spectra.
* New align2D signals.Signal2D 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.
* Signal1D and Signal2D 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:

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

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

* Added TIFF 16, 32 and 64 bits support by using (and distributing) Christoph Gohlke's `tifffile library <https://pypi.org/project/tifffile/>`_.
* 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:

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

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 Signal1D 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.