Commit e9cb0b2c authored by Aaron Bray's avatar Aaron Bray
Browse files

Merge branch '2.x' into feature/respiratory_disease

# Conflicts:
#	test/scenarios/validation/systems/RespiratoryValidation.json
parents f4eb13f1 8c01131d
......@@ -182,6 +182,7 @@ void Nervous::BaroreceptorFeedback()
{
m_BaroreceptorActiveTime_s = 0.0;
m_BaroreceptorFeedbackStatus = true;
Info("Starting Baroreceptor timer ");
}
else
{
......@@ -200,6 +201,8 @@ void Nervous::BaroreceptorFeedback()
}
else
{
if (m_BaroreceptorFeedbackStatus)
Info("Stopping Baroreceptor timer ");
m_BaroreceptorFeedbackStatus = false;
}
......
......@@ -57,11 +57,9 @@ patient/HemorrhageClass2FemoralArtery.json = ScenarioTest
patient/HemorrhageClass2InternalMultiple.json = ScenarioTest
patient/HemorrhageClass2InternalSpleen.json = ScenarioTest
patient/HemorrhageClass2NoFluid.json = ScenarioTest
patient/HemorrhageClass2NoFluidLongTerm.json = ScenarioTest
patient/HemorrhageClass2Saline.json = ScenarioTest
patient/HemorrhageClass3PackedRBC.json = ScenarioTest
patient/HemorrhageClass4NoFluid.json = ScenarioTest
patient/HemorrhageClass4NoFluidLongTerm.json = ScenarioTest
patient/HemorrhageCM1.json = ScenarioTest
patient/HemorrhageCM2.json = ScenarioTest
patient/LobarPneumoniaExacerbation.json = ScenarioTest
......
......@@ -244,7 +244,7 @@ public class SETestConfiguration
}
else if(job.executor.getClass().getName().indexOf("Scenario")!=-1)//Is a Scenario File test
{
deriveScenarioResultNames(job, job.name);
deriveScenarioResultNames(job, job.name);
}
else
{
......@@ -260,7 +260,7 @@ public class SETestConfiguration
List<String> patientFileNames;
if(patientFiles.equalsIgnoreCase("all"))
patientFileNames = FileUtils.findFiles("./patients", sce_ext, true);
patientFileNames = FileUtils.findFiles("./patients", sce_ext, true);
else
{
String[] patientFiles = this.patientFiles.split(",");
......@@ -290,7 +290,7 @@ public class SETestConfiguration
jobs.add(job);
continue;
}
copy = job.clone();
copy = job.clone();
copy.patientFile = pFileName;
deriveScenarioResultNames(copy, copy.name.replaceAll(sce_ext, "-"+pFileName));
jobs.add(copy);
......
......@@ -102,13 +102,13 @@ public class SETestDriver
job.state = SETestJob.State.Comparing;
cThread.job = job;
activeThreads++;
cThread.start();
cThread.start();
break;
}
else
{
job.state = SETestJob.State.Complete;
}
}
}
}
}
......@@ -125,7 +125,7 @@ public class SETestDriver
activeThreads++;
}
if(activeThreads == engineThreads)
break;
break;
}
}
if(activeThreads==0)
......@@ -211,8 +211,8 @@ public class SETestDriver
{
CSVComparison compare = new CSVComparison();
compare.limit = job.percentDifference;
compare.reportDifferences = false;
compare.setFullReportPath(job.reportFiles.get(i));
compare.reportDifferences = false;
compare.setFullReportPath(job.reportFiles.get(i));
if(new File(job.computedFiles.get(i)).exists())
{
Set<String> failures = null;
......
{
"Name": "HemorrhageCM1",
"Description": "Bleeding in the right leg and vena cava, then iv administration.",
"StartType": {
"Description": "",
"StartType":
{
"PatientConfiguration": {
"PatientFile": "StandardMale.json"
}
},
"DataRequestManager": {
"DataRequest": [{
"DecimalFormat": {
"Precision": 1
},
"PropertyName": "Weight",
"Unit": "kg"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "Physiology",
"PropertyName": "HeartRate",
"Unit": "1/min"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "Physiology",
"PropertyName": "HeartStrokeVolume",
"Unit": "mL"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "Physiology",
"PropertyName": "BloodVolume",
"Unit": "L"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "Physiology",
"PropertyName": "ExtravascularFluidVolume",
"Unit": "L"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "Physiology",
"PropertyName": "ArterialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "Physiology",
"PropertyName": "MeanArterialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
},
"Category": "Physiology",
"PropertyName": "SystolicArterialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "Physiology",
"PropertyName": "DiastolicArterialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "Physiology",
"PropertyName": "CardiacOutput",
"Unit": "L/min"
}, {
"DecimalFormat": {
},
"Category": "Physiology",
"PropertyName": "HemoglobinContent",
"Unit": "g"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "Physiology",
"PropertyName": "CentralVenousPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "Physiology",
"PropertyName": "PulmonaryCapillariesWedgePressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 3
},
"Category": "Physiology",
"PropertyName": "TidalVolume",
"Unit": "mL"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "Physiology",
"PropertyName": "TotalLungVolume",
"Unit": "L"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "Physiology",
"PropertyName": "RespirationRate",
"Unit": "1/min"
}, {
"DecimalFormat": {
"Precision": 3
},
"Category": "Physiology",
"PropertyName": "OxygenSaturation",
"Unit": "unitless"
}, {
"DecimalFormat": {
"Precision": 3
},
"Category": "Physiology",
"PropertyName": "CarbonDioxideSaturation",
"Unit": "unitless"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "EndTidalCarbonDioxideFraction",
"Unit": "unitless"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "Physiology",
"PropertyName": "TotalAlveolarVentilation",
"Unit": "L/min"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "Physiology",
"PropertyName": "TranspulmonaryPressure",
"Unit": "cmH2O"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "Physiology",
"PropertyName": "CoreTemperature",
"Unit": "degC"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "Physiology",
"PropertyName": "SkinTemperature",
"Unit": "degC"
}, {
"DecimalFormat": {
"Precision": 3
},
"Category": "Physiology",
"PropertyName": "RespiratoryExchangeRatio",
"Unit": "unitless"
}, {
"DecimalFormat": {
},
"Category": "Physiology",
"PropertyName": "OxygenConsumptionRate",
"Unit": "mL/min"
}, {
"DecimalFormat": {
},
"Category": "Physiology",
"PropertyName": "CarbonDioxideProductionRate",
"Unit": "mL/min"
}, {
"DecimalFormat": {
},
"Category": "Physiology",
"PropertyName": "GlomerularFiltrationRate",
"Unit": "mL/min"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "Physiology",
"PropertyName": "RenalBloodFlow",
"Unit": "L/min"
}, {
"DecimalFormat": {
"Precision": 3
},
"Category": "Physiology",
"PropertyName": "UrineProductionRate",
"Unit": "mL/min"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "LeftAfferentArterioleResistance",
"Unit": "mmHg min/mL"
}, {
"DecimalFormat": {
"Precision": 4
},
"Category": "Physiology",
"PropertyName": "RightAfferentArterioleResistance",
"Unit": "mmHg min/mL"
}, {
"DecimalFormat": {
},
"Category": "GasCompartment",
"CompartmentName": "LeftAlveoli",
"PropertyName": "Pressure",
"Unit": "cmH2O"
}, {
"DecimalFormat": {
},
"Category": "GasCompartment",
"CompartmentName": "LeftAlveoli",
"SubstanceName": "Oxygen",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "GasCompartment",
"CompartmentName": "LeftAlveoli",
"SubstanceName": "CarbonDioxide",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
},
"Category": "GasCompartment",
"CompartmentName": "RightAlveoli",
"PropertyName": "Pressure",
"Unit": "cmH2O"
}, {
"DecimalFormat": {
},
"Category": "GasCompartment",
"CompartmentName": "RightAlveoli",
"SubstanceName": "Oxygen",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "GasCompartment",
"CompartmentName": "RightAlveoli",
"SubstanceName": "CarbonDioxide",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
},
"Category": "GasCompartment",
"CompartmentName": "Carina",
"SubstanceName": "Oxygen",
"PropertyName": "PartialPressure",
"Unit": "cmH2O"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "GasCompartment",
"CompartmentName": "Carina",
"SubstanceName": "CarbonDioxide",
"PropertyName": "PartialPressure",
"Unit": "cmH2O"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "LiquidCompartment",
"CompartmentName": "Aorta",
"SubstanceName": "Oxygen",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "LiquidCompartment",
"CompartmentName": "Aorta",
"SubstanceName": "CarbonDioxide",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "LiquidCompartment",
"CompartmentName": "VenaCava",
"SubstanceName": "Oxygen",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "LiquidCompartment",
"CompartmentName": "VenaCava",
"SubstanceName": "CarbonDioxide",
"PropertyName": "PartialPressure",
"Unit": "mmHg"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "LiquidCompartment",
"CompartmentName": "RightTubules",
"SubstanceName": "Sodium",
"PropertyName": "Concentration",
"Unit": "g/L"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "LiquidCompartment",
"CompartmentName": "LeftTubules",
"SubstanceName": "Sodium",
"PropertyName": "Concentration",
"Unit": "g/L"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "Substance",
"SubstanceName": "Oxygen",
"PropertyName": "AlveolarTransfer",
"Unit": "mL/s"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "Substance",
"SubstanceName": "CarbonDioxide",
"PropertyName": "AlveolarTransfer",
"Unit": "mL/s"
}, {
"DecimalFormat": {
"Precision": 6
},
"Category": "Substance",
"SubstanceName": "Epinephrine",
"PropertyName": "BloodConcentration",
"Unit": "ug/L"
}, {
"DecimalFormat": {
"Precision": 3
},
"Category": "Physiology",
"PropertyName": "SystemicVascularResistance",
"Unit": "mmHg s/mL"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "Physiology",
"PropertyName": "UrineOsmolality",
"Unit": "mOsm/kg"
}, {
"DecimalFormat": {
"Precision": 3
},
"Category": "Physiology",
"PropertyName": "RightTubularReabsorptionFluidPermeability",
"Unit": "mL/s mmHg m^2"
}, {
"DecimalFormat": {
"Precision": 3
},
"Category": "Physiology",
"PropertyName": "LeftTubularReabsorptionFluidPermeability",
"Unit": "mL/s mmHg m^2"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "Substance",
"SubstanceName": "Sodium",
"PropertyName": "BloodConcentration",
"Unit": "g/L"
}, {
"DecimalFormat": {
"Precision": 5
},
"Category": "Substance",
"SubstanceName": "Sodium",
"PropertyName": "Clearance-RenalClearance",
"Unit": "mL/min kg"
}, {
"DecimalFormat": {
},
"Category": "Substance",
"SubstanceName": "Sodium",
"PropertyName": "Clearance-RenalReabsorptionRate",
"Unit": "mg/min"
}, {
"DecimalFormat": {
"Precision": 1
},
"Category": "Substance",
"SubstanceName": "Sodium",
"PropertyName": "MassInBody",
"Unit": "g"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "LiquidCompartment",
"CompartmentName": "Bladder",
"SubstanceName": "Sodium",
"PropertyName": "Concentration",
"Unit": "g/L"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "LiquidCompartment",
"CompartmentName": "RightUreter",
"PropertyName": "InFlow",
"Unit": "mL/min"
}, {
"DecimalFormat": {
"Precision": 2
},
"Category": "LiquidCompartment",
"CompartmentName": "LeftUreter",
"PropertyName": "InFlow",
"Unit": "mL/min"
}]
"DataRequestManager":
{
"DataRequest":
[
{ "DecimalFormat": { "Precision": 1 }, "PropertyName": "Weight", "Unit": "kg" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "HeartRate", "Unit": "1/min" },
{ "DecimalFormat": { "Precision": 1 }, "Category": "Physiology", "PropertyName": "HeartStrokeVolume", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "BloodVolume", "Unit": "L" },
{ "DecimalFormat": { "Precision": 1 }, "Category": "Physiology", "PropertyName": "ExtravascularFluidVolume", "Unit": "L" },
{ "DecimalFormat": { "Precision": 1 }, "Category": "Physiology", "PropertyName": "ArterialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 1 }, "Category": "Physiology", "PropertyName": "MeanArterialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { }, "Category": "Physiology", "PropertyName": "SystolicArterialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 1 }, "Category": "Physiology", "PropertyName": "DiastolicArterialPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "CardiacOutput", "Unit": "L/min" },
{ "DecimalFormat": { }, "Category": "Physiology", "PropertyName": "HemoglobinContent", "Unit": "g" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "CentralVenousPressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "PulmonaryCapillariesWedgePressure", "Unit": "mmHg" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "TidalVolume", "Unit": "mL" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "TotalLungVolume", "Unit": "L" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "RespirationRate", "Unit": "1/min" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "OxygenSaturation", "Unit": "unitless" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "CarbonDioxideSaturation", "Unit": "unitless" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "EndTidalCarbonDioxideFraction", "Unit": "unitless" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "TotalAlveolarVentilation", "Unit": "L/min" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "TranspulmonaryPressure", "Unit": "cmH2O" },
{ "DecimalFormat": { "Precision": 1 }, "Category": "Physiology", "PropertyName": "CoreTemperature", "Unit": "degC" },
{ "DecimalFormat": { "Precision": 1 }, "Category": "Physiology", "PropertyName": "SkinTemperature", "Unit": "degC" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "RespiratoryExchangeRatio", "Unit": "unitless" },
{ "DecimalFormat": { }, "Category": "Physiology", "PropertyName": "OxygenConsumptionRate", "Unit": "mL/min" },
{ "DecimalFormat": { }, "Category": "Physiology", "PropertyName": "CarbonDioxideProductionRate", "Unit": "mL/min" },
{ "DecimalFormat": { }, "Category": "Physiology", "PropertyName": "GlomerularFiltrationRate", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 2 }, "Category": "Physiology", "PropertyName": "RenalBloodFlow", "Unit": "L/min" },
{ "DecimalFormat": { "Precision": 3 }, "Category": "Physiology", "PropertyName": "UrineProductionRate", "Unit": "mL/min" },
{ "DecimalFormat": { "Precision": 4 }, "Category": "Physiology", "PropertyName": "LeftAfferentArterioleResistance", "Unit": "mmHg min/mL" },
{ "DecimalFormat": { "Precision": 4 },