Added .idea folder with PyCharms settings.
Changed icon.ico (now round).
PhaseMap and MagData: Now use h5py to load/save data (via HyperSpy).
Deprecated loading routines (x3d) are gone now!
tests: All tests now reflect this change.
scripts: Streamlined some scripts. Many are now in separate project:
Script-Vault

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.

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

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

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

holoimage: turned off interpolation
test_compliance: added scripts to be tested
setup: work in progress

numcore: deleted c1, c2, c3, name changes in phase_mag_real
analytic: name change beta to phi
phasemapper: changes to include numcore
test_compliance: also checkes .pyx files now
setup: now works properly (hopefully on other systems, too)
compare_discs: added script to compare discs

test_compliance: Added PEP8 TestCase

scripts: changed scripts to work with the new syntax of the package
PhaseMag and MagData: added load and save options for NetCDF files
MagData: changed 3D-plotting to use mayavi (faster and better looking)
test: added more TestCases for various modules
phasemapper: added computation method to use mx and my (now standard)
compare_method_errors: first draft of script to compare the different errors

test: changed the dataloader TestCase
pyramex: first experiments with Cython and SCons
dataloader: changed the order in which the dimensions are saved,
        z_len is no longer part of the magnetization (this was the reason why
        we had to divide by res, which is equal to z_len for calculating coeff)
magcreator: shapes are now separate functions, mag_shape is now an argument for
        one unified create_hom_mag-function
phasemap: unification of the phasemap-functions in real space (just the pixel-
        field is calculated different now)