_pyhum_read bed picking changes

[iannesbitt]

This PR contains a couple of changes:

• KDTree requires a ndarray, not a list as given previously (this was causing an error on a fresh installation)
• Bed picking prompts are moved to the correct places in sequence to avoid delays due to imread
• Timeouts are removed in favor of closing the window or a center mouse click
• Terminal will contain some instructions regarding the previous bullet