NeuralEnsemble/neuroConstruct — pull request #6 by ccluri (2013-05-24 13:10:04+00:00)
Title: HDF5 files saving under variable time step

1) when saving in hdf5 in neuron variable time step (cvode) array size is not equal to number of simulation time steps. the correct measure is v_time.size()
2) (irrespective of cvode) hdf5 file is being overwritten each time a new array is added - because it is opened with 'w' instead of 'a' - switching to 'a' leads to other issues that it has to be deleted each time simulation is re-run. Opting instead to move hdf5file creation to an outer loop. Because of this, there is a change in naming of the hf5file - file name is sim reference - suggest better.
3) (with or without cvode) time values are important in case of non variable time step - these are now dumped in the hdf5 file, the output results in Errors -because of multiple attempts to add /time array - however the file closes correctly.
4) Switch to h5py instead of tables.
5) The above are quick fixes, that do not break current output .dat files - this code-fix is meant to be pointers to bugs (and a bugfix) and can be improved.