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...

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!

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

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

modularity and compatibility with future algorithms and ideas.

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

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

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

magcreator: Added the second angle for the magnetization
reconstructor: Changed method name
all others: Changed "beta" to "phi" to reflect the new angle in magcreator

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

Scripts are nearly adapted to the new structure and easier to read.
(Except analytic module and scripts get_jacobi and inverse)

For Pushing Purposes

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)

Removed old scripts (AnalyticSolution and DataLoader)
Added several template testcases

because Spyder can't create projects in subfolders -.-

jacobi matrix now contains the derivatives instead of descriptive strings

Added a fitting icon

PYRAMID: PYthon based Reconstruction Algorith for MagnetIc Distributions
Separated Igor files from PYRAMID files
moved all files one folder higher

analytic: changed analytic solution for discs (still not perfect)
magcreator: added logo function
phasemap: revised the analytical formulas -> more uniform
added new folder for PYRAMID project
added testsuite module

Holoimaging and phasemap now have separate display functions
Display_combine implemented in main.py
Changed sqrt(x^2 + y^2) to np.hypot(x,y)
magcreator now uses <= instead of <
pdb starts on error (implemented in main.py)

Changed the way parameters are given to magcreator functions (now as tuples)
Implemented the real space approach to get phase images (works, but slow!)