forward_model: DistributedForwardModel created which uses the multiprocessing
               package for distributed computations.

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...

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!

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

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

kernel, phasemapper: now use the new pyramid.fft module.
MagData, PhaseMap: now use np.float32 instead of np.float64
MagData: new quiver_plot3d with just matplotlib (buggy and still WOP).
logging: deleted several logging.debug prompts for speed up.
util: deleted module!

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

Added a steppest descent minimizer for lp problems and added an experimental split-bregman optimizer.

        m: i'm'age
        n: i'n'put

fixed some minor compilation bugs and updated to current jutil. prepared jutil reconstruction routines.

Still to do: PhaseMapperElectric does not work
             3D reconstruction does not converge

New structure with (hopefully) no redundancy.

minor changes to plotting methods (PhaseMap now plottable without colorbar).
phase_map: gain can now be set to 'auto' (5 fringes, determined by max. phase).
renamed 'density' to 'gain' (makes more sense).
regularisator: started to include norms and more kinds of regularisations.
mag_slicer: GUI which can go through loaded magnetizations along the major axes.
paper 1: minor changes to the scripts for the results.

Many Doctring corrections, all plots now have a "show" parameter to not show a
plot at the end of the method (needed for guis and such).
magdata: quiver_plot: axis switch for x-projection, implemented logarithmic
         arrows and scaling feature.
projector: added to_mag_data() method to directly produce a projected
           magnetization distribution.
gui/create_logo: removed (obsolete and unuseful).
gui/mag_slicer: added!

regularisator: new module to represent different regularisation strategies
costfunction: changed to use the new Regularisator classes, changed arguments!
dataset: fixed bug that always displayed the own phase maps instead of provided
reconstruction: changed to use the new Regularisator classes, changed arguments!
scripts/rueffner_file: tried to avoid Memory Error (no success)
scripts/zi_an: added holographic contour plots with overlayd magnetization
scripts/reconstruction_sparse_cg_test: now uses Regularisator classes and plots
                                       phase differences (original - reconstr.)