bbfrederick/rapidtide: January 6, 2020 checkpoint release

I had a lot of changes checked in, and thought I'd do what I think is the last checkin before 2.0. Highlights of this release are a completely revamped, multpass version of happy that does mask estimation and artery detection automatically; total reimplementation of the correlation calculation and fitting as classes to encapsulate the functionality a lot better and have cleaner interfaces (and also many fixes, optimizations an features), and a major improvement to tide pool, adding display of the probe regressor. This turns out to be very useful, as I found problems in my filter implementation which will be fixed in 2.0. Another big first is that now I've added a Dockerfile, so you can download a containerized version of rapidtide with all the optional dependencies! That should make this more accessible to a wider range of groups. This is the last release that will support Python 2.x Detailed changes follow. Version 1.9 (1/6/20) (all): Now compatible with nibabel 3.x (all): Significantly expanded test suite. Code coverage is now at 47%. (documentation): Added instructions for installing the deep learning filter code (documentation): Numerous tweaks and fixes (docker): There is now a containerized version of the rapidtide package, which avoids a lot of installation woes (rapidtide2x, showxcorrx): Completely replaced correlation and fitting routines with faster, more robust (and more rigorously tested) versions (rapidtide2x, showxcorrx): Enhancements to the permutation methods (rapidtide2x, showxcorrx): Revised internals to guarantee xcorr scale matches values (rapidtide2x, showxcorrx): Improved fitter performance in edge cases (thin peaks, symmetric around max) (rapidtide2x, showxcorrx): Changed limits to avoid crash when peak is at edge of range (rapidtide2x, showxcorrx): Fixed some (but apparantly not all) dumb errors in calls to null correlation calculations. (rapidtide2x): Implemented workaround for unknown crasher in GLM filtering when nprocs != 1 (rapidtide2x): Added experimental respiration processing (rapidtide2x): Fixed an uncaught bug in bipolar processing. (rapidtide2x): Setting ampthresh to a negative number between 0 and 1 sets the percentile of voxels to use for refinement (rapidtide2x): Support for new minimum sigma limit in correlation fit (rapidtide2x): Fixed a bug that caused fit fails on very narrow peaks, added diagnostic info (rapidtide2x): Putting in scaffolding to support phase randomization for null correlation calculation. (rapidtide2x): Properly specify correlation limits in null correlation and accheck (rapidtide2x): Slight modifications to pickleft routine to avoid a rare bug (rapidtide2x): Masks should now be properly generated for zero mean and non-positive definite data. (rapidtide2x): Tweaked the autocorrelation correction (rapidtide2x): Added an error check to avoid crashing when no significance tests are nonzero (rapidtide2x): Added upper and lower sigma limits to peak fitting uss to match new class (showxcorrx): Updated to match rapidtide2x fitting (showxcorrx): Enhanced error reporting (showxcorrx): Added width range tests (showxcorrx): Added norefine option, output more debugging info (showxcorrx): Set validity limits for gaussian fit (happy, rapidtide2x): Fixed a bug in output nifti header parameters (copy headers by value, not reference!) (happy): New multipass architecture allows much better results - initial passes set estimation masks and find potential arterial voxels. (happy): Aliased correlation integrated into happy as experimental feature (happy): Fixed a conceptual error in how I normalized projected timecourses (happy): Added brain cine output (happy): If estmask is supplied, us it. If not, generate a vessel mask and repeat final steps. (happy): Added option to detect and invert arterial signals, improved time output. (happy): Shorten pulse recon step size to 10 ms (happy): Better envelope handling, fixed bug in timecourse phase projection. (happy): Some changes to improve performance with long TRs (happy): Added happy paper reference (happy): Increased gridbins (used in phase projection): default to 2 after testing showed lower noise than 1.5 bins (happy): Added ability to pad cyclically rather than reflecting around the ends (happy): Added ability to smooth projection in the phase direction (on by default) (happy): Significant improvements to GLM processing (spatial and temporal versions, aliased temporal correlation) (happy): Added "checkpoint" option to dump more intermediate data for debugging. (happy): Added more progress bars, and the ability to turn them off. (happy): Print out version info at runtime. (tidepool): Major update with new functionality (tidepool): The probe regressor, it's spectrum, and how it was filtered are now shown in the main window (tidepool): Properly disable atlas buttons when no atlas is loaded, avoiding crashes (tidepool): Removed support for pyqt4 (tidepool): Some UI tweaks (tidepool): Added some infrastructure for future support for loading multiple runs (tidepool): New atlases to suport fmriprep default coordinates (tidepool): Numerous bug fixes (ccorrica): Added the ability to oversample the data prior to crosscorrelation (showtc): Added ability to select a column from a multicolumn file as input. (showtc): Can now select a column from multicolumn input text files for each vector. (showtc): Changed the specification of colors and legends. Internal code cleanup. (happy2std): New tool to align happy maps (happywarp): Improvements in filtering (aligntcs): You can now specify single columns out of multicolumn files (showxy): Initial support for specifying color names (spectrogram): Cleanup, added some configuration options (simdata): Some reformatting, updates, and improvements (simdata): Put some data in the example directory to use with simdata (fingerprint): New addition to the library to decompose delay maps using vascular territory templates (fingerprint): Added canonical HCP template maps to the distribution (helper_classes): Added freqtrack class (correlate.py): Added rudimentary mutual information calculation (correlate.py): Multiple aliased correlation methods added, depending on demeaning. (io.py): Fixed support for named columns in BIDS tsvs (io.py): Relaxed requirements for required fields in BIDS jsons (io.py): Added a few convenience routines for dealing with NIFTI files (io.py): Fixed import of parser_func