The PhaseMapperCharge was updated

See merge request !4

test charge finished

See merge request !3

PhaseMapperCharge has been updated.

See merge request !2

test

See merge request !1

docs: moved up one level.
plottools: added some default label sizes.
version: added to VCS and added a TODO (switch to Git)
fielddata: added rot90 for ScalarData, lot of small changes.

Started working on reader for binary ovf files (WIP).
utils.pm now works with PhaseMapperFDFC.

fielddata and phasemap: Now use the new plottools module, cleanup of arguments
                        and documentation.
plottools: New module for pretty plotting and different annotations like text,
           colorwheels and colorbars.
colors: Colorbar now has a black circle outline and arrows pointing in cardinal
        directions.
diagnostics: Small documentation fixes and naming 'avg' --> 'avrg'.
docs: Renewed documentation.

diagnostics: now takes magdata as input instead of a vector.
             Plotting routines for diagnostics added.
fielddata: Added quiverkey if b_0 is provided.
phasemap: If appropriate unit is provided, will be labeled as "Gain Map".
scalebar: Cleaned up and clipping added.

reconstruction: jutil.TakeTime is now used here.
scalebars: Module which allows nice scalebars to be displayed in all plots.
           This is the new default and can be turned off.
ramp: Now stores everything from the dataset directly to self, instead of
      keeping a reference to the DataSet (construct without Dataset in future!).
projector: tqdm now uses tqdm_notebook if used in IPython Notebook!
magcreator: Added functionality for smooth vortices (see de Graef et al.).
kernel: Corrected behaviour of slab geometry (u and v were still switched!).
dataset: phasemappers now accessable as dictionary or list. The append function
         now also takes lists (but projectors and phasemappers can in turn not
         set directly anymore). Se_inv will be updated automatically.
diagnostics: Functionality to access total, directional and magnitude error,
             according to Kemp et al.

dataset: implemented save/load features in io_dataset.py
h5py: copied data from hdf5 files to make sure they exist after file is closed.
projector/phasemap/dataset: force dim/dim_uv to be tuples.

Projectors now have tqdm options to show progress.

phasemap: Now supports flips, rotations and shifts with ndimage.
          Added plot_phase_with_hist to plot histograms (for difference plots).
fielddata: FieldData now properly plots contours and masks (new).
dataset: set_3d_mask now uses the new mask capability of FieldData.
         Default is no longer "logical backprojection".
io_phasemap: Now includes .tif (although that does not always work).
setup.py: Deleted deprecated depencencies.
Renamed a few plot commands to plot_...
Rollback to RdBu as colormap (back from Spectral).

fielddata: slices now include z-component which will be plotted in plot_field.
colors: Minor tweaks. Mainly for Rec. 601/709 input.
phasemap: Now uses 'Spectral' as a colormap.

Now uses an improved cubehelix colorwheel for most purposes.
Other variants are also provided.
Removed hue_mode.

fielddata: Added plot_quiver_field convenience function.
io_phasemap: Added functionality for images separately from HyperSpy.
phasemap: Automatically normalise confidence.
projector: Quaternion for tilt around x-axis corrected (was falsely around y).
reconstruction: Added verbose option (True by default).
reconstruction_2d_from_phasemap: Plotting optimised.

Renaming of variables in PhaseMapperRDFC.jac_T_dot to make more sense...

phasemapper: PhasemapperRDFC: Now the adjoint is calculated correctly (switched
        slicing order, took conjugate of kernel FFTs, deleted superfluous minus
        sign). Results are the same, but calculation is now CORRECT!
fft: Correction of numpy rfftn_adj.
fielddata: Added option for uniform color specification.

kernel: u and v are switched and now finally correct.
        get_elementary_phase is also switched and corrected.
phasemapper: added PhaseMapperCharge from Feng Shan.
forward_model: now uses y instead of phase_vec/Se_inv and now direct properties.
costfunction: corrected some docstrings and documentation comments.
fielddata: corrected some missing integer divisions (// instead of /),
        added plot_streamline().