bunch_index returns the array with the positions (index) of the non-empty bunches, to be used with Beam.not_empty iterator.
bunch_mean, bunch_std and bunch_emit now iterate only over non empty bunches.

Take into account length

CavityResonator.init_phasor is now CavityResonator.init_phasor_track
New CavityResonator.init_phasor uses analytic formula
Fix phase slipping factor for initialization case (rf frame should be delta = (self.wr - self.m*self.ring.omega1))

fix init

Fix mpi_share_distributions

This avoid to store a huge amount of data in all cores before calling mpi_init to share it to all the cores.

Add options to plot beamdata vs index and in streak plot mode
Add setting of colorscale for plot_cavitydata

CavityResonator.init_phasor is now CavityResonator.init_phasor_track
New CavityResonator.init_phasor uses analytic formula
Fix phase slipping factor for initialization case (rf frame should be delta = (self.wr - self.m*self.ring.omega1))

fix init

Fix bug when buffer_size=1 in TuneMonitor by switching to init buffer_count to 0. Now total_size should be 1 less.
Improve plot_tunedata

# Conflicts:
#	tracking/monitors/plotting.py

Fix plot_profiledata error due to change to center instead of bins
Fix plot_cavitydata legends and turn selection

Fix profile monitor
Add detune to cavity monitor

Can compute the CSR impedance for free space and parallel plates model.
WakeFunction not implemented yet.

Wrong data shared in Beam.mpi_share_distributions
Old names in CavityResonator.track corrected

Add a dict_dtype optional parameter to Monitor.monitor_init to allow to choose the dtype to use to save the data.
Improve CavityMonitor to allow for saving beam and cavity phasor for all bunches
Add a plot_cavitydata function
Fix a bug on CavityResonator.track -> nturn += 1 at correct time
Change CavityResonator.track to allow for monitoring the cavity/beam phasor at each bunch

Allow to read both wake function and impedance with read_IW2D_folder
Fix yokoya_elliptic function

# Conflicts:
#	tracking/element.py

Change back invariant name to cs_invariant
Simplify SkewQuadrupole track method

Add comments.
Remove usage of bins, use only center.

Not needed any more due the SynchrotronRadiation change.

Fix bug on Beam.distance_between_bunches for the last bunch when the first bunches are empty.
Change Beam.distance_between_bunches to compute the array only at initalization with Beam.update_distance_between_bunches
Beam.mpi_share_distributions can now share all bunch dimensions.

Correct time decay !
Now ok versus for loop (decay then beam loading)

Typo in the type of data to share for bunch profile. Not sure if there was an effect.

In track method of cavity resonator, there was an additional phasor decay of bin length.
To avoid that the good boundaries are set bins[0] instead of center[0].
For now the bins are also shared in Beam.mpi_share_distributions

Add single core tracking for CavityResonator
Correct missing ref_frame is CavityResonator.track
Change phase of generator voltage to be the bin phase
Correct generator phase for non integer m
Change init_phasor track time to 10 times
Change phasor_evolution k to change order of steps

Add phasor initialization (on the "rf" reference)
Change beam phasor evolution to allow for "beam" or "rf" reference

Correct case when where is no mp in the bin
Remove useless test

Add tracking to CavityResonator based on the mbtrack implementation but using a analytic formula for speed-up
Add method to Beam to share longitudinal distributions
Add methods to Mpi to look for next and previous bunches
Add start of a CavityMonitor, to improve to deal with multi-cores