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Merge branch 'feature/respiratory_disease' of https://gitlab.kitware.com/physiology/engine into feature/respiratory_disease

Hardening respiratory compliance calculation to handle ~0 pressure.

Merge branch 'feature/respiratory_disease' of https://gitlab.kitware.com/physiology/engine into feature/respiratory_disease

Random tweaks and update to chest wall compliance calculation to prevent weirdness with conscoius respiration.

FYI - RespiratoryDriver test is not working at this point

Fix testing for new patient setup

Adding a SEPatient object for the initial patient (healthy stabilized values)

Updated respiratory and anesthesia machine circuit diagrams.
Updated some data flow diagrams.
Tweaked some main page verbiage.

# Conflicts:
#	engine/cpp/physiology/Respiratory.cpp

Added a simple logger to reduce build complexity
Added ability to disable building Java utils

Tune pneumothorax CV effects.

Add Secondary Baroreceptor Effects

See merge request !25

(cherry picked from commit 13c44737)

Rachel Clipp authored Sep 19, 2019 and Aaron Bray committed Oct 09, 2019

(cherry picked from commit 0ebeb6a5)

Rachel Clipp authored Sep 04, 2019 and Aaron Bray committed Oct 09, 2019

Cleaned up the barorector functionality a bit and commented out the sedation dampening effect until I have better validation data.

(cherry picked from commit 8ba9907c)

Rachel Clipp authored Aug 29, 2019 and Aaron Bray committed Oct 09, 2019

Created a member variable for the mean pressure patient baseline so that I only change the baroreceptor setpoint. Shifted the UpdateBaroreceptorThreshold function to before calculating the total baroreceptor setpoint at each timestep.

(cherry picked from commit 6a487e14)

Rachel Clipp authored Aug 26, 2019 and Aaron Bray committed Oct 09, 2019

Added baroreceptor functionality for second order effects, the baroreceptors become less responsive to the blood pressure changes as time passes. Sedation level dampening of the parasympathetic and sympathetic curve slope.

(cherry picked from commit d3668021)

Jeff Webb authored Sep 12, 2019 and Aaron Bray committed Sep 30, 2019

Small fix to action log output.

Jeff Webb authored Sep 09, 2019 and Aaron Bray committed Sep 30, 2019

Updated the anesthisia machine circuit to use pressure sources for supplying gases, rather than flow sources.  Flow sources cause weird pressures in systems that also include pressure sources.

Jeff Webb authored Sep 06, 2019 and Aaron Bray committed Sep 30, 2019

Added some new respiratory specific scenarios.
Removed end tidal co2 from stabilization criteria.

Jeff Webb authored Aug 26, 2019 and Aaron Bray committed Sep 30, 2019

Updated some general math exponentail functions.