Added the fields submodule with field, shapes and vectors!
Added the vis module (not viz) with colors, decorators, plot2d, tools.
Added version.
Minor changes in pyramid.

fielddata: fixed tests!

projector: RotTiltProjector now ends in the correct coord system!
diagnostics: Refined the LCurve class (now saves stuff!)
lorentz: Added preliminary Lorentz imaging functions!

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.

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.

projector: RotTiltProjector implemented!
quaternion: New module providing quaternions!

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

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

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

magdata: implemented save_to_x3d (Bielefeld collaboration)
template.x3d: template for the x3d output (header file with spin-blueprints)
numcore.kernel_core: implemented multiply_jacobi_T_core
scripts: added vtk scripts for full nanowires and segments
         script to process file by Daniel Rüffner

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

phasemapper: added Kernel helper class with methods to calculate the jacobi
matrix or to multiply a vector with the (transposed) jacobi matrix without
explicitly calculating the full matrix
magcreator: added Shape.ellipsoid
numcore: added (experimental) speed-up for jacobi-matrix (not faster)
scripts: modified get_jacobi to test the new Kernel class,
tests: test_compliance now also searches and creates a list of TODOs