Fixed bugs in labels
- They were created when I deleted get_pore_labels
Various changes to run_script, some doc string changes
Introduced new method call to_mask()
- this takes a list of pores or throats and returns a boolean mask with Trues at the given locations
- I have remove the 'return_indices' option from the code. This is now the ONLY option.  If you need a mask, use to_mask