Changed the way the parameters are passing to ptycho.ptycho2D - directly passing amplitudes, positions and initial probe and obj. Example changed accordingly.
Parameters of the update (regularisastion constan <reg_const> in Thibault2009 and learning constant <learning_const> in Maiden2009) can be now passed explicitely in p.Run(). Example updated accordingly.
Minor fixes.
1) Optimisation of the positions added - RefinePos and RefinePosUpdate (combining refinement with ptycho updates). 2) Direct minimisation function and derivatives -directmin_f and directmin_f_der - incorporated into the ptycho module.