Rapidtide

* I have now synced all of the changes in rapidtide2x back to rapidtide2.
* rapidtide now has multiprocessing support using the --multiproc flag. This can cause a dramatic increase in processing speed on multicore/processor machines.
* Dispersion calculation is now off by default.
* Tidepool is now compatible with both PyQt4 and 5.
* Reordered some memory allocation and deallocation to keep the RAM footprint down.
* Some additional significant speedups (support for ffftw if present, caching hamming windows).
* Added an optional cross-spectral density filter for adaptive timecourse filtering. This is a work in progress - not really ready for general use.
* Skeleton of support for Wiener deconvolution to sharpen the correlation function (off by default, not ready for general use).

* I decided to stop hedging and actually commit myself - this is version 1.0.0 - out of beta!
* To promote stability, new features will be put into test versions (the name of the program will have an "x" appended). This way I can do major internal changes and have them available to users without breaking something they might rely on. The "x" versions will sync with the "normal" versions after extensive testing.
* Major new feature (rapidtide2x only for now). Multiprocessing! Significant speedup when using the --multiproc option on machines with multiple cores.
* showxcorrx has new features and defaults.
* Memory allocation has been reorganized to reduce footprint (rapidtide2x).
* Changed imports for better compatibility when running in the NITRC-CE environment (rapidtide2x).
* rapidtide2std now supports nonlinear alignment.
* histnifti is added to the distribution.
* I've added some additional outputs to rapidtide2 and rapidtide2x during refinement to help figure out if the brain is a dispersive filter. This doesn't change how rapidtide2 does the refinement - it's just informational at this point.
* Added spatialfit to the distribution. I use this to analyze delay maps. More on this later.
* Fully implemented samplerate and sampletime options (rapidtide2)
* Corrected and enhanced the use of alternative correlation weighting functions (PHAT, Liang, and Eckart weighting) (rapidtide).
* Updated all scripts for compatibility with matplotlib 2.0.
* Fixed tidepool for compatibility with the new version of pyqtgraph.
* Significant enhancements to showstxcorr (this is a work in progress).
* Example data is no longer installed in the python directory (this never made sense to do).
* Added code to do matched filtering of regressors with mean PSD and/or cross-spectral density. It works, but doesn't do much (rapidtide2x).

* Added code to allow runtime memory profiling if memory_profile library is present.
* Extensive casting of variables to lower memory footprint and allow future optimizations.
* Added explicit garbage collection to reduce memory usage.
* Added optional single precision calculation mode to lower memory footprint.
* Added a second script, "rapidtide2x" where I can distribute and test new features without breaking the main code branch.
* Did some speed optimizations in findmaxlag, including faster gaussian fitting and new MUCH faster parabolic fitting (still experimental).
* Minor bug fixes, code reorganization and cleanup.

* Fixed a bug in the GLM filtering code - if spatial filtering was applied in rapidtide2, the smoothed data was filtered rather than the original data.
* Added an option in rapidtide2 ("--glmsourcefile=FILE") to apply GLM filter to a different dataset than the one used to estimate the delays (this is used for HCP data - the "hp2000_clean" data has had LFO signals partially removed and may compromise delay estimation, so that should be done on the un-"FIX"ed data).
* Added the ability to detect autocorrelation properties of the test regressor that may cause delay estimation to fail with the "--accheck" flag.
* Added an option "--acfix" to try to correct for bad test regressor autocorrelation properties. This is not yet working correctly.
* Added the ability to specify a slicetimes file ("--slicetimes=FILE") if slicetime correction has not yet been applied to the dataset. Not fully tested.
* (rapidtide2std, tidepool) Added the ability to transform and display functional data to highres anatomic space in addition to MNI152 space.
* Various small bugfixes and format cleanups.

* I think I've resolved the issue of crashes due to numba functioning differently on machines other than mine.
* Fixed a masking bug in tidepool that was due to numbers being very close to, but not exactly, 1.
* Made a number of internal changes to rapidtide2 and tidepool to allow dynamic significance masking (not yet working - actually failing spectacularly for the most part, but it's currently commented out).
* Added showstxcorr to the distribution.
* Added the ability to set the mask threshold for correlation and global mask inclusion (this turns out to be needed if you use non-skull-stripped data.)
* Put in some code to start to figure out how to account for dispersion in the delay function.
* Moved the "start movie" button in tidepool to better align with the numerical spin boxes.
* showtc has gotten a significant upgrade in functionality, adding the ability to display power spectra, phase spectra, and set the sample rate to make the x-axis correct.
* Lots of internal formatting/style fixes, and fixed some formatting in the usage statements and documentation.

* Fixed a critical bug that had been introduced in the last round of changes to findmaxlag.
* Disabled numba for findmaxlag (it seems to cause problems for some users).
* New option --skipsighistfit to omit fitting a Johnson SB function to the significance histogram.
* Fixed the usage statement.
* Fixed a bug that set ampthresh to zero when not doing significance estimation.