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.

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

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

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.)

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

(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)