A system provides heart ablation unit control. The system includes an input processor for acquiring electrophysiological signal data from multiple tissue locations of a heart and data indicating tissue thickness at the multiple tissue locations. A signal processor processes the acquired electrophysiological signal data to identify location of particular tissue sites of the multiple tissue locations exhibiting electrical abnormality in the acquired electrophysiological signal data and determines an area of abnormal tissue associated with individual sites of the particular sites. An ablation controller automatically determines ablation pulse characteristics for use in ablating cardiac tissue at an individual site of the particular tissue sites in response to the acquired data indicating the thickness of tissue and determined area of abnormality of the individual site.