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.

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.

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

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)

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!

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!

tests: implemented the missing TestCases!
dataset: mask is now created if not given!
phasemapper: guaranteed np.float32 format for RDRC (expected by Cython)
projector: now uses fft.FLOAT

pep8: optimizations
phasemapper_core: numcore module for phasemapper
scripts: compatibility with new structure
reconstruction: new scripts

Renames:
datacollection --> dataset
optimizer      --> reconstruction

scripts:
interactive_setup is now implemented in an extended Spyder startup file.
some other scripts are now
the rest is NOT adapted, yet, which is the next task at hand
furthermore scripts will be sorted and unused ones deleted in the next commit

regrid: Added many scripts for regridding by Jörn
logging: Introduced logging
scripts: Added Scripts for regridding and simulating stuff for cooperations
removed: Unused test scripts
structure: Many new restructuring aspects already implemented