Update plotting formating

Changes for plotting in most tools to make plots look consistent across tools. Added new plotting functions for MTP and treatment optimization.

JMP: No changes

MTP: Changes:

Change colors to use matlab default colors.
Change joint moment plot to have moments without SynX be dashed lines. This plot now has 3 lines per window: Mtp with no synx, mtp with synx, and experimental.

New:

Added a new function plotMtpHillTypeMuscleParamsCompare which takes 2 results directories and compares their muscle model parameters.

NCP: Changes:

Switched color orders so that experimental is blue and ncp output is orange to be consistent with the rest of the pipeline.

GCP: Changes

Switched colors to be matlab default colors
Added legends
Changed figure sizes
Added figure window names to easily distinguish between figures
No longer use the plotNumber argument. This argument is still accepted to not break old code, but it does nothing.

Treatment Optimization: Changes:

Added figure window names similar to GCP.
Merged plot torque and synergy controls into one function to plot controls. This new function also allows multiple files to be passed into the function as a list of files (useful for plotting DO results). The old functions are still around so as to not break anyone's existing code.

New:

Added a function plotTreatmentOptimizationResultsFromSettingsFile that plots treatment optimization results when given a settings file as an argument. This function does not plot muscle activations yet.

rcnl-org / nmsm-core