1. A method for imaging a breast of a patient, the method comprising: (a) taking three-dimensional (3D) cone-beam breast computed tomography (CBBCT) projection image data of the breast; (b) processing the projection image data taken in step (a) in a computing device for pre-reconstruction correction of the projection image data; (c) performing cone beam reconstruction of a matrix of 3D distribution of a linear attenuation coefficient of the breast in the computer device; (d) performing correction and processing after the reconstruction of the matrix of the breast in the computer device; (e) storing the corrected reconstruction matrix into an image archive device; (f) using a CPU-based computer device and a GPU-based computer device to perform the following plurality of tasks: detecting and characterizing mass, detecting calcifications, assessing breast density and detecting and characterizing duct system of the breast, based on the reconstructed 3D data; (g) outputting the composite breast information including locations, shapes and size(s) of mass(es) and calcifications, number of calcifications in volume of interest, breast density measurement and shapes of duct system of the breast; and (h) outputting the probability of malignancy of the breast based on the composite breast information determined in (g); wherein step (d) comprises: (a) detecting the skin of the breast and to remove the skin of the breast from the image data; (b) applying a stepwise fuzzy clustering algorithm in the computing device to the image data with the skin removed to adaptively cluster image voxels in the image data; (c) dividing the image data in the computing device into a plurality of categories; and (d) forming a three-dimensional image in the computing device from the image data divided into the plurality of categories.