The Pierre Auger Observatory operative in Argentina, studies the ultra-high energy cosmic rays with energies above 1018eV. The atmosphere is also monitored by a collection of different instruments. In this paper we present a study on the retrieval of the cloud coverage from the atmospheric monitoring data collected by the four IR cloud cameras placed in the sites of the Observatory. We discuss two different algorithms that supply pixel by pixel cloudiness information in the form of binary masks. The final objective of the study is collecting different algorithms to obtain a reliable set that allow to overcome most of the more frequent ambiguities due to particular cloud configurations and atmospheric conditions during the acquisitions. This can support the cloudiness masks already provided by the AUGER data base.