Rapidtide

* (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 maximum 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 imports

* (documentation) Added description of rapidtide output files.
* (tide_funcs) Fixed a VERY old bug in detrend that added an offset to the detrended timecourse. The effect of the bug on rapidtide2(x) is probably small, because we almost always use data that has already been detrended. The effect in some very particular use cases, though, was large enough that I finally noticed it after 3 years.
* (rapidtide2, 2x) Added option to disable progress bars (good when saving output to a file).
* (rapidtide2, 2x) Improved output to memusage file.
* (rapidtide2, 2x) Report fit errors with better granularity.
* (rapidtide2, 2x) Allow specification of external correlation mask.
* (rapidtide2, 2x) Added "MTT" map to hopefully remove the effect of autocorrelation.
* (rapidtide2, 2x) Added some additional diagnostic information to significance estimation.
* (rapidtide2x, tide_funcs) Major changes to peak fitting to try to improve stability using new findmaxlag_gauss_rev function.
* (rapidtide2x, tide_funcs) Moved logmem function to tide_funcs so that it's available for other programs.
* (rapidtide2x) Fixed bug when running despeckling on a single processor.
* (rapidtide2, 2x) Attempting to stabilize the lagsigma measurement with better initial parameter estimates.
* (tide_funcs) Cast timecourse index as a long to avoid an overflow in NIRS timecourses.
* (rapidtide2, 2x, tide_funcs) Added ability to set searchfrac in fits.
* (rapidtide2, 2x) Disable threshold during significance estimation, simplify internal logic for turning on estimation.
* (rapitdide2) Fixed bug in mask generation
* (showtc) Added the ability to select columns to plot, and to read BIDS style json/tsv.gz physiological files
* (showtc, showxy) Updated colormap names for compatibility with matplotlib 2.2+
* (rapidtide2std) Initial support for warping with ANTs (does not work yet)
* (rapidtide2std) Added the ability to align a single file.
* (tidepool) Support for MTT map.
* (ccorrica, showstxcorr) PEP 8 reformatting.
* (testing) Added test for findmaxlag versions.
* (testing) Added test for stxcorr functions.
* (temporaldecomp) Allow 3D masks.
* (atlastool) Changed method for generating 3D files.
* (atlastool) Various bug fixes in 3D atlas generation.
* (resamp1tc) Modernized option selection, Added nodisplay option.
* (showstxcorr) Explicit integer cast of indices.
* (showstxcorr) Removed initial Hamming window.
* (showstxcorr) Added csv output of matrices.
* (linfit) Added to distribution.
* (tide_funcs) Changed value of rcond in leastsq to be compatible over multiple versions of bumpy (least. comprehensible. note. ever.)
* (tide_funcs) Added findexecutable and isexecutable functions
* (tide_funcs) Added a convolution gridding function
* (tide_funcs) Fixed readvec(s) so that is now works properly if a text file ends with an empty line.
* (tide_funcs) Added function to read slice times from a BIDS sidecar file.
* (spatialdecomp, temporaldecomp) Command line is now saved.
* (threeD) Added

* (documentation) Fixed some formatting.
* (showxcorrx) Cleaned up usage statement.

* (rapidtide2, 2x) Added macros to support setting multiple options at once.
* (rapidtide2, 2x) --nirs macro sets a number of parameters to be appropriate for NIRS data processing.
* (rapidtide2, 2x) --venousrefine macro sets refinement parameters to use data only from large draining veins (only works reliably in healthy subjects ATM).
* (rapidtide2, 2x) Now tabulate maximum correlation times without range limit for my own secret, diabolical purposes.
* (rapidtide2, 2x) Fixed a bug that was not shifting all of the timecourses if they were not in the refinement mask.
* (rapidtide2, 2x) Improved memory usage tracking.
* (rapidtide2, 2x) Reduced memory footprint.
* (rapidtide2, 2x) Move large arrays into shared memory for multiprocessor jobs to avoid duplicating RAM.
* (rapidtide2, 2x) You can now set the number of processors used (rather than always using all of them) when multiprocessing.
* (rapidtide2, 2x) Properly shut down worker procedures to free RAM earlier.
* (rapidtide2, 2x) Fixed a bug in the initialization of the dispersion calculation.
* (rapidtide2, 2x) Fixed a maddening bug in output of the refinement mask.
* (rapidtide2, 2x) Fixed the range on the Gaussian filtering progress bar.
* (rapidtide2, 2x) Made some improvements to the despeckling procedure.
* (rapidtide2, 2x) --refinepasses is now deprecated - use --passes instead.
* (rapidtide2, 2x) Added new methods to specify the sample rate (or sample time) of the input data file.
* (rapidtide2, 2x) Revised usage statement to make parameter names better reflect their function.
* (rapidtide2, 2x) A lot of internal code cleanup and dead code removal.
* (rapidtide2, 2x, showxcorrx) Allow specification of the correlation window function (hamming (default), hann, blackmanharris, or None).
* (showtc) Cleaned up some bugs introduced during the last overhaul.
* (tcfrom3col) Added to package (generates a timecourse from an FSL style 3 column regressor file.
* (tidepool) Default to displaying using the valid mask rather than the p<0.05 mask.
* (tidepool) Enabled usage of the refine mask.

* (rapidtide2, 2x) Added new option, '--despeckle', which uses a spatial median filter to find and correct points where the correlation fit picked the wrong autocorrelation lobe. This dramatically improves the quality of the output maps. This will probably be turned on by default in the next release.
* (tidepool) FINALLY fixed the click positioning bug. Worth the update just for this. That was driving me crazy.
* (tidepool) Formatting improvements.
* (tidepool) Preliminary support for multiple territory atlases and averaging modes in tidepool.
* (tidepool) Atlas averaging is now (mostly) working.
* (rapidtide2, 2x) Now support text format NIRS datasets (2D text files) in addition to NIFTI fMRI files.
* (rapidtide2, 2x) Substantial internal changes to reduce memory footprint, improve speed.
* (rapidtide2x, showxcorrx) Initial support added for Choudry's cepstral analysis method for delay calculation.
* (showtc) Substantial improvements (improved formatting, ability to specify separate subplots, transpose input, line colors, waterfall plots, offsets between lines, titles, etc).
* (rapidtide2std) Internal code cleanup.
* (showxy) Now supports multiple input files.
* Added glmfilt to package to filter 1D or 4D data out of 4D datasets.
* Added spatialdecomp to do spatial PCA decomposition of 4D NIFTI files.
* Added temporaldecomp to do temporal PCA decomposition of 4D NIFTI files.
* Added ccorrica to the distribution to provide cross correlation matrices between all timeseries in a 2D text files.
* Added atlastool to aid in preparation of atlas files for tidepool.

* New release to trigger a Zenodo DOI.
* Fully tested for python 3.6 compatibility.
* Added linfit to the distribution.
* Set a limit of 25 dispersion regressors.
* Reformatted the documentation somewhat.
* Added some recipes to the documentation for common use cases.
* Cleaned up and fixed the resampling code.
* Minor quality and speed improvement to timeshift.
* No longer output "datatoremove" to save space.
* Removed some redundant screen refreshes from tidepool.
* Reorganized and removed dead code.
* Changed default mode for calculating refined regressors to "unweighted_average".
* Synced changes in rapidtide2x to rapidtide2