bbfrederick/rapidtide: September 2018 checkpoint release

Version 1.6 (9/19/18) (whole project) Cleanup and reorganization (tsalo). (documentation) Major revisions to clean things up (tsalo). (workflows) Initial creation (work in progress) (tsalo). (testing) Reorganized and fixed - now it actually works! (tsalo). (coverage) Code coverage for testing is now tracked (21% - we can improve significantly with workflows) (tsalo). (rapidtide2, 2x, happy) Finally found (and fixed) the reason for a range of random stalls and slowdowns when running on a cluster. MKL extensions were silently distributing some numpy calculations over all cores (which means running N jobs running on a cluster tried to use N^2 cores - not good at all...). The maxiumum number of MKL threads is now settable on the command line, and defaults to 1 (no multiprocessor numpy). Strangely, this makes everything a little faster in single processor mode, and A LOT faster in multiprocessor mode. (tide_funcs.py) tide_funcs.py has been split into filter.py, fit.py, io.py, miscmath.py, resample.py, stats.py, and util.py. All executables fixed to match. (rapidtide2, 2x) Oversample factor is now set automatically by default to make the correlation timestep 0.5 or less. This dramatically improves fits for longer TRs (> 1.5 seconds). (rapidtide2, 2x) Moved the major passes (null correlation, correlation, correlation fit, refine, wiener filter and glm) into separate modules for maintainability and to simplify tinkering. (rapidtide2, 2x) Isolated multiprocessing code to make speeding up new routines easier and avoid massive code duplication. (rapidtide2, 2x) Fixed some bugs in correlation mask reading and saving include and exclude masks. (rapidtide2, 2x) Improved tmask, fixed a bug. (rapidtide2, 2x, glmfilt) Made glmpass more general so it could be used in other scripts) (resamp1tc, resample.py) Added arbresample, modified dotwostepresample. (fit.py) Added Kaiser Bessel window function. (io.py) savetonifti now properly sets output data type in header. (io.py) Added routine to read in motion timecourses. (filter.py) Consolidated doprecalcfftfilt and xfunc into transferfuncfilt. (filter.py) Added new "complex" spectrum option. (filter.py) Added docstrings, code cleanup and regularization. (filter.py) Added new 'spectrum' routine. (filter.py) Initial support for precalculated arb filtering. (resample.py) Adjusted gridding to be symmetric around output value. (util.py) Reimplemented valtoindex to make it faster. (showtc) Updated to use new spectrum routine. (spectrogram) added to distro. (rapidtide2, 2x, resamp1tc showxcorr, showxcorrx, showstxcorr) eliminated all use of Butterworth filters by default. (spatialfit) Fixed numpy import