The Intra-Pulse Multi-Energy (IPME) method of material discrimination mitigates main disadvantages of the traditional “interlaced” approach: ambiguity caused by sampling different regions of cargo and reduction of effective scanning speed. A novel concept of creating multi-energy probing pulses using a standing-wave structure allows maintaining a constant energy spectrum while changing the time duration of each sub-pulse and thus enables adaptive cargo inspection. Depending on the cargo density, the dose delivered to the inspected object is optimized for best material discrimination, maximum material penetration, or lowest dose to cargo. A model based on Monte-Carlo simulation and experimental reference points were developed for the optimization of inspection conditions.