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[fmrisim] Improve simulator (#150) * Add TDA initial script. * Added documentation * Added documentation * Added documentation * Added the test_tda * Simulator initial commit. Includes the simulator function with the tests and examples * Error in uploading simulator * Updated simulator based on edits. Added two condition example. Removed TDA code. * Updated names, improved comments, changed load procedure for mask * Updated simulator * Updated the way TDA features are generated * Updated tests for new simulator code * Updated fmrisim test, corrected error of deleting test_hpo * No need to make any change to hyperparamopt * Updated doc string * Conforming to PEP8 * Removed nibabel * Increased test coverage * Updated for PEP8 * Updated for pep8 * Updated for pep8 * Updated pep8 * Edited the tests * Complexity tests updating * Updated tests
[reprsimil] Mostly bug fixing for brsa (#144) * a Changes to be committed: new file: brainiak/brsa/test.txt * deleted: brsa/test.txt * changed some of the logging levels * Creating new functions to prepare to a new version which explicitly deals with shared time series not explained by design matrix * Further changing singpara, preparing to deal with shared time series X0 * Changed the model to consider spatial correlation in noise * Updated the BRSA model to incorporate spatial correlation in noise Fixed some bugs in utils.ReadDesign Renamed epsilon to eta in consistence with the paper Expanded the example a bit Other minor changes * fixed some bugs and typos * Removed some redundant calculation" * changed some of the logging levels * Creating new functions to prepare to a new version which explicitly deals with shared time series not explained by design matrix * Further changing singpara, preparing to deal with shared time series X0 * Changed the model to consider spatial correlation in noise * attempt to solve conflict Changes to be committed: modified: brainiak/reprsimil/brsa.py modified: brainiak/utils/utils.py modified: examples/reprsimil/brsa_representational_similarity_estimate_example.ipynb modified: tests/reprsimil/test_brsa.py modified: tests/utils/test_utils.py * fixed some bugs and typos * Removed some redundant calculation" * Removing some unnecessary package in brsa example * adding comment on nuisance regressor * removing outdated note in brsa * updating docstring * a bit more changing of docstring * minor changes * update the example for brsa * updating example to do z-scoring * cleaning up * cleaning up * fix a bug in utils.ReadDesign * bug fixing for BRSA._prepare_data_XYX0 * trivial * changes re PR review