Commit 889348c3 authored by Aaron Bray's avatar Aaron Bray
Browse files

Merge branch '3.x' into feature/ventilator_validation

# Conflicts:
#	src/cpp/cpm/physiology/Respiratory.cpp
parents 18b431b4 2d697ebc
......@@ -33,7 +33,7 @@ set(CMAKE_DEBUG_POSTFIX "d")
set_property(GLOBAL PROPERTY USE_FOLDERS ON)
project(Pulse VERSION 3.0.0 LANGUAGES C CXX)
project(Pulse VERSION 3.1.0 LANGUAGES C CXX)
#-----------------------------------------------------------------------------
# Project install directories
......@@ -126,7 +126,7 @@ if(MSVC)
# Using MD as that seems to be what I run into alot, you could change these to /MT and /MTd if you want...
set(CMAKE_CXX_FLAGS_DEBUG "/D_DEBUG /MDd /Zi /Ob2 /Oi /Od /RTC1 /MP /EHsc" CACHE STRING INTERNAL FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "/MD /MP /EHsc" CACHE STRING INTERNAL FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "/MDd /Zi /MP /EHsc" CACHE STRING INTERNAL FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "/MD /Zi /MP /EHsc" CACHE STRING INTERNAL FORCE)
endif()
if ( CMAKE_COMPILER_IS_GNUCC )
# Protobuf is not using the same variable name in its swap specificiation definitions
......
{
{"Scenario": {
"Name":"BasicStandard",
"Description":"Basic scenario measuring patient vitals with no insults or interventions",
"EngineStateFile":"./states/StandardMale@0s.pbb",
......@@ -93,4 +93,21 @@
{"DecimalFormat":{"Precision":2}, "Category":"LiquidCompartment","CompartmentName":"Pericardium","PropertyName":"Pressure","Unit":"mmHg"}
]},
"AnyAction":[{"AdvanceTime":{"Time":{"ScalarTime":{"Value":2.0,"Unit":"min"}}}}]}
\ No newline at end of file
"AnyAction":[{"AdvanceTime":{"Time":{"ScalarTime":{"Value":2.0,"Unit":"min"}}}}]},
"Configuration": {
"AutoSerialization": {
"Directory": "./states/testing/",
"Filename": "patient/HemorrhageVaryingSeverity",
"AfterActions": "On",
"Period": {
"ScalarTime": {
"Value": 5.0,
"Unit": "s"
}
},
"PeriodTimeStamps": "On",
"ReloadState": "On"
}
}
}
......@@ -7,6 +7,7 @@ add_external_project_ex( Dirent
URL "https://github.com/tronkko/dirent/archive/1.23.2.zip"
URL_HASH MD5=43514791ab73ef5ac7c490afc7c3bab2
CMAKE_CACHE_ARGS
-DBUILD_TESTING:BOOL=OFF
-DDIRENT_BUILD_TESTS:BOOL=OFF
RELATIVE_INCLUDE_PATH ""
DEPENDENCIES ""
......
......@@ -4,8 +4,8 @@
include(AddExternalProject)
define_external_dirs_ex( Eigen3 )
add_external_project_ex( Eigen3
URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz"
URL_HASH MD5=9e30f67e8531477de4117506fe44669b
URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.9/eigen-3.3.9.tar.gz"
URL_HASH MD5=609286804b0f79be622ccf7f9ff2b660
CMAKE_CACHE_ARGS
-DBUILD_TESTING:BOOL=OFF
RELATIVE_INCLUDE_PATH ""
......
......@@ -14,8 +14,8 @@ endif()
include(AddExternalProject)
define_external_dirs_ex(protobuf)
add_external_project_ex( protobuf
URL https://github.com/protocolbuffers/protobuf/releases/download/v3.12.2/protobuf-all-3.12.2.zip
URL_MD5 ec63c1566640a5873566e76ec8eb1398
URL https://github.com/protocolbuffers/protobuf/releases/download/v3.14.0/protobuf-all-3.14.0.zip
URL_MD5 82cba836a6085599fae030d6c071d4a3
SOURCE_SUBDIR ./cmake
CMAKE_CACHE_ARGS
-DBUILD_SHARED_LIBS:BOOL=OFF
......
......@@ -20,7 +20,7 @@ Threads=-1
#UseStates=true
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
# Time stamp periods is creating a file per save and using the time stamp as naming convention
#AutoSerialization=./states/testing/,5,On,On,On
#AutoSerialization=./states/testing/,0,On,On,On
Executor=com.kitware.pulse.cdm.testing.CDMUnitTestDriver
Executor=com.kitware.pulse.engine.testing.EngineUnitTestDriver
......@@ -31,4 +31,4 @@ Macro EngineUnitTest=EngineUnitTestDriver FastPlot Baseline=unit_tests/pulse/ Co
Macro EngineUnitTestFull=EngineUnitTestDriver FullPlot Baseline=unit_tests/pulse/ Computed=./test_results/unit_tests/pulse
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
patient/BasicStandard.json = ScenarioTest
patient/BasicStandard.json =
\ No newline at end of file
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\ No newline at end of file
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\ No newline at end of file
......@@ -20,13 +20,13 @@
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "TidalVolume", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "RespirationRate", "Unit": "1/min" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "OxygenSaturation", "Unit": "unitless" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "VenaCava", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "RightHeartVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "VenaCava", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "RightHeart", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "SystemicVascularResistance", "Unit": "mmHg s/mL"},
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "TotalHemorrhageRate", "Unit": "mL/s"},
......
......@@ -20,13 +20,13 @@
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "TidalVolume", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "RespirationRate", "Unit": "1/min" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "OxygenSaturation", "Unit": "unitless" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "VenaCava", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "RightHeartVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "VenaCava", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "RightHeart", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "SystemicVascularResistance", "Unit": "mmHg s/mL"},
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "TotalHemorrhageRate", "Unit": "mL/s"},
......
......@@ -20,13 +20,13 @@
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "TidalVolume", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "RespirationRate", "Unit": "1/min" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "OxygenSaturation", "Unit": "unitless" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "VenaCava", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "RightHeartVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "VenaCava", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "RightHeart", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "SystemicVascularResistance", "Unit": "mmHg s/mL"},
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "TotalHemorrhageRate", "Unit": "mL/s"},
......
......@@ -20,13 +20,13 @@
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "TidalVolume", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "RespirationRate", "Unit": "1/min" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "OxygenSaturation", "Unit": "unitless" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "VenaCava", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "RightHeartVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "VenaCava", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "RightHeart", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "SystemicVascularResistance", "Unit": "mmHg s/mL"},
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "TotalHemorrhageRate", "Unit": "mL/s"},
......
......@@ -20,13 +20,13 @@
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "TidalVolume", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "RespirationRate", "Unit": "1/min" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "OxygenSaturation", "Unit": "unitless" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "VenaCava", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "RightHeartVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "SubstanceName": "Oxygen", "PropertyName": "PartialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "MyocardiumVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "BrainVasculature", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "VenaCava", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "LiquidCompartment", "CompartmentName": "RightHeart", "PropertyName": "InFlow", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "SystemicVascularResistance", "Unit": "mmHg s/mL"},
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "TotalHemorrhageRate", "Unit": "mL/s"},
......
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