Smooth_vortex now can have a homogeneous core with radius larger 1.
Hacky solution for PyQt4/5, change later!

Changed ignore files.

docs: moved up one level.
plottools: added some default label sizes.
version: added to VCS and added a TODO (switch to Git)
fielddata: added rot90 for ScalarData, lot of small changes.

fielddata and phasemap: Now use the new plottools module, cleanup of arguments
                        and documentation.
plottools: New module for pretty plotting and different annotations like text,
           colorwheels and colorbars.
colors: Colorbar now has a black circle outline and arrows pointing in cardinal
        directions.
diagnostics: Small documentation fixes and naming 'avg' --> 'avrg'.
docs: Renewed documentation.

diagnostics: now takes magdata as input instead of a vector.
             Plotting routines for diagnostics added.
fielddata: Added quiverkey if b_0 is provided.
phasemap: If appropriate unit is provided, will be labeled as "Gain Map".
scalebar: Cleaned up and clipping added.

reconstruction: jutil.TakeTime is now used here.
scalebars: Module which allows nice scalebars to be displayed in all plots.
           This is the new default and can be turned off.
ramp: Now stores everything from the dataset directly to self, instead of
      keeping a reference to the DataSet (construct without Dataset in future!).
projector: tqdm now uses tqdm_notebook if used in IPython Notebook!
magcreator: Added functionality for smooth vortices (see de Graef et al.).
kernel: Corrected behaviour of slab geometry (u and v were still switched!).
dataset: phasemappers now accessable as dictionary or list. The append function
         now also takes lists (but projectors and phasemappers can in turn not
         set directly anymore). Se_inv will be updated automatically.
diagnostics: Functionality to access total, directional and magnitude error,
             according to Kemp et al.

dataset: implemented save/load features in io_dataset.py
h5py: copied data from hdf5 files to make sure they exist after file is closed.
projector/phasemap/dataset: force dim/dim_uv to be tuples.

phasemap: Now supports flips, rotations and shifts with ndimage.
          Added plot_phase_with_hist to plot histograms (for difference plots).
fielddata: FieldData now properly plots contours and masks (new).
dataset: set_3d_mask now uses the new mask capability of FieldData.
         Default is no longer "logical backprojection".
io_phasemap: Now includes .tif (although that does not always work).
setup.py: Deleted deprecated depencencies.
Renamed a few plot commands to plot_...
Rollback to RdBu as colormap (back from Spectral).

fielddata: slices now include z-component which will be plotted in plot_field.
colors: Minor tweaks. Mainly for Rec. 601/709 input.
phasemap: Now uses 'Spectral' as a colormap.

Now uses an improved cubehelix colorwheel for most purposes.
Other variants are also provided.
Removed hue_mode.

fielddata: Added plot_quiver_field convenience function.
io_phasemap: Added functionality for images separately from HyperSpy.
phasemap: Automatically normalise confidence.
projector: Quaternion for tilt around x-axis corrected (was falsely around y).
reconstruction: Added verbose option (True by default).
reconstruction_2d_from_phasemap: Plotting optimised.

Addition of plot_field for FieldData as alternative to quiver plots.
PhaseMap phase plot now has an option to cut outliers (e.g. difference plots).
IO of PhaseMaps now can handle different file extensions in one loading.
Phasemap creator GUI now uses IO loading.
Replaced flatten with ravel (memory efficiency).
Renamed non constant variables to lower case (not UPPER CASE anymore).

fielddata: Now takes figsize as argument
phasemap: phase_plot now uses imshow (much faster)
Removed API (to determine later...)

New API module unclutters the namespace (import pyramid.api as pr).

phasemapper: Now without fft.shift (not necessary thanks to fft.fftfreq)
magcreator: Now vortices with orientation along negative axes possible.
fielddata: HDF5 load updated to new HyperSpy BaseSignal (all signal axes now...)

GUIs now import .ui-files directly.

Refactoring: Replaced MagData with VectorData and added ScalarData class (and common superclass FieldData).
magnitude is now called field (which is more appropriate)
projector now uses FieldData to process both vector and scalar data (foundation was in place before)

fieldconverter: methods to convert M to A to B
magdata: a bit more parameters for quiver_plot3d(), added contour_plot3d()
phasemapper: pm() extended for different projections (not just simple)
kernel: u and v switched (now named after the unit magnetization direction, which makes much more sense)

Added PyCharm files!
Commit before Reformatting with PyCharms!

Added .idea folder with PyCharms settings.
Changed icon.ico (now round).
PhaseMap and MagData: Now use h5py to load/save data (via HyperSpy).
Deprecated loading routines (x3d) are gone now!
tests: All tests now reflect this change.
scripts: Streamlined some scripts. Many are now in separate project:
Script-Vault

colormap: Added TransparentColormap.
magdata: Added get_magslice method, to_emd and from_emd.
phasemap: Added to_emd and from_emd.
gui: New GUI "PhaseMap Creator".
tests: Moved from ./tests to ./pyramid/tests. Not a package anymore!

semper: Implements the SemperFormat class for phasemaps and magnetizations.
forwardmodel: Docstrings for DistributedForwardModel.
phasemap: save_to_text now optionally without header.
ramp: Docstrings added.

Cleanup and documentation!
ramp: New class for polynomial ramps. Instantiated in the ForwardModel.
forwardmodel: Now uses new ramp class.
phasemapper: Ramp functionality moved to ramp class.
reconstruction: Ramp order not used, ramp can be now retrieved from the ramp
                class after reconstruction.
analytic, magcreator: Better and consistent definition of pixel centers and
                      their influence on the phase.
testing: Minor corrections for new syntax.

colormap: New module with colormap subclass which has special functions to
          calculate directional rgb-colors, now used in many plots!
__init__: On star import now also has abbreviations for a few modules.
fwd_model: Now has flags for fitting an offset and/or ramp.
           CAUTION: will be moved next update to new class!
magdata: Removed colorwheel stuff (all moved to 'colormap'). Overhaul of quiver
         plot in 2D and 3D. Now shows mask and uses new colormap for angular
         color coding.
phasemap: Now uses the new colormap for holo plots. Removed color wheel (moved
          to the new class). Added function to add ramps.
phasemapper: Now handles also offsets and ramps in the phase.
             CAUTION: will be moved next update to new class!
projector: Fixed bugs in SimpleProjector. 1) leftmost pixels are no longer moved
           moved to left corner of padded projection (when dim_uv is not None).
           2) odd padding when using dim_uv are now handled properly (one more
           pixel on top and right if necessary).
costfunction: n is now taken from the fwd_model instead of the data_set.
dataset: Introduced the count variable which gives the number of images.
magcreator: In the process of updating, more on next commit.
reconstruction: Also handles ramps and offsets now, properly extracts them after
                reconstruction.
regularisator: New argument 'add_params' is used to cut off input (for offset
               and ramp) which are not used in the regularisation.
scripts: several small changes...

Phase maps now also have a mask and a confidence matrix.
Began new script structure (temporary folders created).
Cleanup, logging and documentation done.
config: NTHREADS is now set here.
dataset: Method for creating 3D masks added.
phasemap: Mask and confidence matrix added. Padding and cropping supported.
forwardmodel: Stubs for multiprocessing added (next TODO!).
kernel: Added support for perturbed reference wave.
magdata: Padding and cropping supported.
projector: New property 'sparsity' introduced.
regularisator: Stub for ComboRegularisator added (next TODO!).
tests: Changed accordingly.

magdata: added convenience functions for flipping and rotating of magnetic
         distributions, fixed bug with ar_dens.
phasemap: now also has a mask which will be used to construct a 3D-mask for the
          magnetic distribution during reconstruction. Added setter/getter.
          Added copy(), scale_down()/scale_up() convenience functions.
          !CAUTION! Only NetCDF4 files save every new parameter!
projector: Fixed hidden bug in X/YTiltProjector, which was problematic during
           tilts over 360°. Now uses linear algebra (much clearer!).
           get_info() function now can be used non-verbose (for filenames).
dataset: added several setter/getter, addes set_3d_mask() for simple 2D tasks,
         renamed mask to confidence (for Se_inv construction)
tests: updated to include the fixes and new functions introduced in this update!

magdata/phasemap: load and save methods now dynamically save with absolute and
        relative paths. Relative paths are defined in the config.py file!

docstrings: updated!
costfunction: CFAdapterScipyCG obsolete, deleted estimate_lambda()
dataset: use_fftw and threads obsolete
diagnostics: implemented stuff... much stuff...
fft: Docstrings and implementation of threads
magcreator: fixed bug in slab (dimension mix-up)
phasemap: plot now also returns colorbar
reconstruction: PrintIterator and optimize_simple_leastsq obsolete
regularisator: Docstrings
scripts: minor modifications
scripts - reconstruct_random_pixels: now use optimize_linear
testcases: analytic, compliance, kernel, magcreator, magdata, projector

Se_inv: is now handled differently, defaults to eye-matrix, but can be set
        later (added a few convenience functions to DataSet)
utility: (re-)added utility module for index conversion
kernel/phasemapper: can now use FFTW library and operate on pre-allocated
        arrays
dtype: set dtype of arrays to np.float32/np.complex64 (halves memory size),
       also applied to numcore routines!
magdata: quiver_plot can now plot every n-th arrow (yet untested!)
reconstruction scripts: modified several reconstruction scripts.

setup: Changes to setup.py, pyramid.version to fit to numpy and jutil
       now uses __all__ magic and supports from pyramid import *
tests: changes to test_compliance/magcreator/analytic (should now work)
collaborations: added several scripts for Patrick
reconstruction: added batch file for the reconstruction of several configs
test methods: (unfinished) scripts for fftw tests and kernel comparisons
paper 1: ch5-4 changed padding values to 0, 1, 3 and 7
plotting: deleted plt.show() lines (have to be done manually now or via Spyder)
logging: now named _log instead of LOG (private variable instead of constant)
         also some logs were disabled, because Pylint says they are slow...
reconstruction: now has info argument (pass a list in which cost info is copied)
phasemapper: changed sign of constant PHI_0, is now correctly positive (instead
             the negative z-integration is taken into account which was not done
             before!)
kernel: now uses FFTW, numpy code was changed accordingly and is still available
phasemapper: also uses FFTW now, work in progress: FFTW for jac_T_dot