GUIs now import .ui-files directly.

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!

costfunction: Now takes a ForwardModel as input instead of DataSet.
forwardmodel: New private function for processing one image (multiprocessing).
magdata: Quiver Plots (2D/3D) now support color encoding (angle or amplitude).
         Private method for creating the appropriate colormap.
reconstruction: Now takes Costfunction as argument instead of DataSet.
regularisator: Introduced ComboRegularisator.
scripts: New scripts.

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.

package: some minor corrections (mainly import statements), some old functions
         were revived (e.g. in MagData)

scripts: adaption to the new structure and sorting (more work is to do here...)

_version: __version__ string is now imported from this file

phasemapper_core.pyx: added to separate the corresponding numcore_functions
                      from kernel_core.pyx

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

pyramid: all docstrings in numpydoc (package installed) format (used by spinx)
holoimage: removed error, phase was falsely multiplied by pi/2
magcreator: removed create_mag_dist_comb, renamed functions for disc and vortex
magdata: Allows creation of empty MagData objects and easy adding of magnitudes
phasemap: Allows units to be set for plots, added 3D plot
phasemapper: Electrostatic component implemented
projector: Projection now includes thickness profile
docs: support for html, latex and pdf (experimental), use "make *" in shell
scripts: new structure, deleted some compare_* functions, added test_methods
.hpignore: now also ignores *.c and _* files (_build used in docs)

setup.py: Final cleanup
deleted initpyximport, compare_method_errors and get_revision (now in setup.py)

jacobi matrix now contains the derivatives instead of descriptive strings