briandrawert/pyurdme — pull request #7 by ahellander (2014-03-07 06:18:57+00:00)
Title: Threejstest

getSpecies can slice efficiently in the hdf5 dataset U. Load time and memory usage of say one species at a given timepoint dramatically improved. Internally, the layout of the data i U have changed again. For a given timepoint, the dofs are U[i,:], where 0...Ncells-1 is species A, Ncells...2Ncells-1 speceis B etc.

Postprocessing routinges may need to change to accomodate for this (unless using getSpecies).

Now there are two routes to accessing data
1.) getSpecies - partial IO, never store U in result object. Memory lean.
2.) U = result["U"], same behavior as before. U added to result object.