BOWTrainer 'blends' image features

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I'm using the BOWTrainer class to cluster multiple segments of texture classes to create a texton dictionary and class models. For this i'm first using the .add method to add the 1d texture segments to the object then using the .cluster method to generate the cluster centres.

I'm having issues with classifier accuracy and wanted to confirm whether this class works by clustering the segments separately? I'm worried that if i'm adding textures with distinct lines,(like bricks), that these could loose their definition if they're clustered together?

Thanks