Summary of edits:

0. datasets/dense_design_matrix.py
        - added stamps parameter and functionality to DenseDesignMatrix class
1. datasets/preprocessing.py
        - implemented keep_var_fraction option in PCA class
        - added classes: ExtractPatchesWithPosition (creates stamps) and ExtractPatchPairs (reads stamps)
        - removed duplicate CentralWindow class
2. pca.py
        - removed extraneous calls to _update_cutoff (now only called by _PCABase.train)
        - added keep_var_fraction parameter and functionality