The criteria for measuring music similarity are important for developing a flexible music recommendation system. Some data-driven methods have been proposed to calculate music similarity from only music signals, such as metric learning based on a triplet loss using tag information on each musical piece. However, the resulting music similarity metric usually captures the entire piece of music, i.e., the mixing of various instrumental sound sources, limiting the capability of the music recommendation system, e.g., it is difficult to search for a musical piece containing similar drum sounds. Towards the development of a more flexible music recommendation system, we propose a music similarity calculation method that focuses on individual instrumental sound sources in a musical piece. By fully exploiting the potential of data-driven methods for our proposed method, we employ weakly supervised metric learning to individual instrumental sound source signals without using any tag information, where positive and negative samples in a triplet loss are defined by whether or not they are from the same musical piece. Furthermore, assuming that each instrumental sound source is not always available in practice, we also investigate the effects of using instrumental sound source separation to obtain each source in the proposed method. Experimental results have shown that (1) unique similarity metrics can be learned for individual instrumental sound sources, (2) similarity metrics learned using some instrumental sound sources are possible to lead to more accurate results than that learned using the entire musical piece, (3) the performance degraded when learning with the separated instrumental sounds, and (4) similarity metrics learned by the proposed method well produced results that correspond to perception by human senses.