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

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.)

projector: ALL projectors can now handle arbitrary dimensions
dataset: reverted to old strategy (dimensions must match)
reconstruction: least square method now also with regularization of order 1
scripts: cleanup and streamlining, added projector_test

dataset: phase map dimensions do not have to match anylonger
        (just with the connected projector)
reconstruction: simple least square: added regularisation of 1. order
scripts: stuff which will be cleaned up in next commit

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

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

not represent the correct matrizes (hopefully, now they do).

>>> PACKAGE
forwardmodel, kernel, phasemapper:
        b_0 is now again inherent part of the kernel.
projector:
        Corrected .jac_T_dot, now delivers product for the correct matrix.
>>> SCRIPTS
simple_reconstruction:
        Does simple compliance tests for 1 and 2 projections and tests a simple
        solver via scipy.sparse.linalg.cg for the reconstruction.

documentation: minor changes and updates of docstrings

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

modularity and compatibility with future algorithms and ideas.

(At the moment a bit slow, optimization with Cython seems necessary).

Replaced res with a for the grid spacing
(resolution is a reserved word in electron microscopy
Work in progress: jacobi matrix for projection

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

phasemapper: new function get_kernel() for convenience, mag_real_fast() for
calculation of the phase with pre-computed lookup-tables
projector: single_tilt_projection() now works as intended
Added scripts for the creation of core-shell-structures
Added script for charge calculation by contour integration
Added script for creating tilt series of core-shell-structure for reconstruction
Various minor modifications, mostly nomenclature and streamlining

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)

holoimage: changed colorwheel (now without axes)
magcreator: create_vortex now also allows a 3D-center (2D is extracted)
magdata: new methods: get_mask() and scale_down()
phasemap: changed plotting defaults (new kwargs)
phasemapper: started on electrical contribution

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