* fixed rotate with reshape=True
 * 2d rotation: fix sign of x component
 * clip: negative values are no longer cut off for scalars
 * re-organized tests and fixtures
 * improve coverage: clip, __getitem__, rotate: scalars, comparisons, ...

Co-authored-by:  <d.weber@fz-juelich.de>
Co-authored-by:  <j.caron@fz-juelich.de>

Last working one is test_mask(), the rest is currently TODO

Co-authored-by: Alexander Clausen <a.clausen@fz-juelich.de>
Co-authored-by: Jan Caron <j.caron@fz-juelich.de>

Added the fields submodule with field, shapes and vectors!
Added the vis module (not viz) with colors, decorators, plot2d, tools.
Added version.
Minor changes in pyramid.

fielddata: fixed tests!

projector: RotTiltProjector now ends in the correct coord system!
diagnostics: Refined the LCurve class (now saves stuff!)
lorentz: Added preliminary Lorentz imaging functions!

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!

semper: Implements the SemperFormat class for phasemaps and magnetizations.
forwardmodel: Docstrings for DistributedForwardModel.
phasemap: save_to_text now optionally without header.
ramp: Docstrings added.

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.

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!

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