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adding new induction howto for paper
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‎projects/howto/InductionDemo/src/HowTo-induction.cpp‎

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/**************************************************************************************
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Copyright 2015 Applied Research Associates, Inc.
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Licensed under the Apache License, Version 2.0 (the "License"); you may not use
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this file except in compliance with the License. You may obtain a copy of the License
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at:
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http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing, software distributed under
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the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
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CONDITIONS OF ANY KIND, either express or implied. See the License for the
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specific language governing permissions and limitations under the License.
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**************************************************************************************/
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#include "HowTo-induction.h"
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#include <iostream>
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// Include the various types you will be using in your code
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#include <biogears/cdm/compartment/SECompartmentManager.h>
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#include <biogears/cdm/engine/PhysiologyEngineTrack.h>
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#include <biogears/cdm/patient/assessments/SEArterialBloodGasAnalysis.h>
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#include <biogears/cdm/patient/SEPatient.h>
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#include <biogears/cdm/patient/actions/SEHemorrhage.h>
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#include <biogears/cdm/patient/actions/SEPainStimulus.h>
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#include <biogears/cdm/patient/actions/SESubstanceBolus.h>
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#include <biogears/cdm/patient/actions/SESubstanceCompoundInfusion.h>
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#include <biogears/cdm/patient/actions/SESubstanceInfusion.h>
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#include <biogears/cdm/properties/SEScalarTypes.h>
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#include <biogears/cdm/substance/SESubstanceManager.h>
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#include <biogears/cdm/system/physiology/SEBloodChemistrySystem.h>
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#include <biogears/cdm/system/physiology/SECardiovascularSystem.h>
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#include <biogears/cdm/system/physiology/SERenalSystem.h>
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#include <biogears/cdm/system/physiology/SERespiratorySystem.h>
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#include <biogears/cdm/utils/SEEventHandler.h>
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#include <biogears/engine/BioGearsPhysiologyEngine.h>
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#include <biogears/string/manipulation.h>
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#include <filesystem>
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namespace fs = std::filesystem;
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int main(int argc, char* argv[])
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{
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// To run multiple hemorrhages
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double lowestBloodFlow_mL_Per_min = 50.0;
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double highestBloodFlow_mL_Per_min = 200.0;
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double flowIncrement = 25.0;
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std::filesystem::path states = "./states";
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std::string state;
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for (const auto& dirEntry : fs::recursive_directory_iterator(states, std::filesystem::directory_options::skip_permission_denied)) {
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std::cout << dirEntry << std::endl;
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state = dirEntry.path().filename().string();
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std::string logName = "./inductionData/HowToHemorrhagepHValidation";
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logName.append(state);
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logName.append(".log");
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InductionThread induction(logName, state);
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induction.AdministerInduction();
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}
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}
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}
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using namespace biogears;
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InductionThread::InductionThread(const std::string logFile, std::string stateFile)
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: m_inductionThread()
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{
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//Create the engine and load patient state
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m_bg = CreateBioGearsEngine(logFile);
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m_bg->GetLogger()->Info(asprintf("Initiating %f %s", logFile, "% hemorrhage flow rate, for patient"));
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std::string statePath = "./states/";
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statePath.append(stateFile);
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m_bg->GetLogger()->Info(statePath);
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if (!m_bg->LoadState(statePath)) {
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m_bg->GetLogger()->Error("Could not load state, check the error");
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throw std::runtime_error("Could not load state, check the error");
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}
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//Create CSV results file and set up data that we want to be tracked (tracking done in AdvanceModelTime)
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std::string resultsFileInduction = std::to_string(dochem);
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std::string resultsFile = "./inductionData/HowToInduction";
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resultsFile.append(resultsFileInduction);
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resultsFile.append(stateFile);
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resultsFile.append(".csv");
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//Load substances and compounds
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SESubstance* vas = m_bg->GetSubstanceManager().GetSubstance("Vasopressin");
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SESubstance* lactate = m_bg->GetSubstanceManager().GetSubstance("Lactate");
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//we will perform a 1:1:1 infusion ration during our mtp
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SESubstanceCompound* ringers = m_bg->GetSubstanceManager().GetCompound("RingersLactate");
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SESubstanceCompound* blood = m_bg->GetSubstanceManager().GetCompound("Blood_ONegative");
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SESubstanceCompound* plasma = m_bg->GetSubstanceManager().GetCompound("Plasma");
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SESubstanceCompound* platelets = m_bg->GetSubstanceManager().GetCompound("PlateletsInfusion");
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//Create infusion and bolus actions
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m_ringers = new SESubstanceCompoundInfusion(*ringers);
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m_blood = new SESubstanceCompoundInfusion(*blood);
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m_plasma = new SESubstanceCompoundInfusion(*plasma);
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m_platelet = new SESubstanceCompoundInfusion(*platelets);
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m_VasopressinBolus = new SESubstanceBolus(*vas);
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//initialize trackers to 0
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m_ivBagVolume_mL = 0.0;
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m_ivBagVolumeBlood_mL = 0.0;
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m_ivBagVolumePlasma_mL = 0.0;
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m_ivBagVolumePlatelet_mL = 0.0;
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m_bg->GetEngineTrack()->GetDataRequestManager().SetResultsFilename(resultsFile); //deposits in build/runtime
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("HeartRate", "1/min");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreateSubstanceDataRequest().Set(*vas, "PlasmaConcentration", MassPerVolumeUnit::ug_Per_L);
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("ArterialBloodPH", "unitless");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("CardiacOutput", "mL/min");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("InflammatoryResponse-TissueIntegrity");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("MeanArterialPressure", "mmHg");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("SystolicArterialPressure", "mmHg");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("DiastolicArterialPressure", "mmHg");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("EndTidalCarbonDioxideFraction", "unitless");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("RespirationRate", "1/min");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("GlomerularFiltrationRate", "mL/min");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("TidalVolume", "mL");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("SystemicVascularResistance", "mmHg s/mL");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("StrongIonDifference", "mmol/L");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("BloodVolume", "mL");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("MeanUrineOutput", "mL/hr");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreatePhysiologyDataRequest().Set("PainVisualAnalogueScale");
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m_bg->GetEngineTrack()->GetDataRequestManager().CreateLiquidCompartmentDataRequest().Set("VenaCava", *lactate, "Molarity", AmountPerVolumeUnit::mmol_Per_L);
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m_bg->GetEngineTrack()->GetDataRequestManager().CreateLiquidCompartmentDataRequest().Set("Aorta", "OutFlow", VolumePerTimeUnit::mL_Per_min);
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m_bg->GetEngineTrack()->GetDataRequestManager().CreateSubstanceDataRequest().Set(*lactate, "Clearance-RenalClearance", VolumePerTimeMassUnit::mL_Per_min_kg);
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m_bg->GetEngineTrack()->GetDataTrack().Probe("totalFluid_mL", m_TotalVolume_mL);
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m_bg->GetEngineTrack()->GetDataTrack().Probe("bagVolume_mL", m_ivBagVolume_mL);
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m_bg->GetEngineTrack()->GetDataTrack().Probe("bagVolumeBlood_mL", m_ivBagVolumeBlood_mL);
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m_bg->GetEngineTrack()->GetDataTrack().Probe("bagVolumePlasma_mL", m_ivBagVolumePlasma_mL);
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m_bg->GetEngineTrack()->GetDataTrack().Probe("bagVolumePlatelet_mL", m_ivBagVolumePlatelet_mL);
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m_runThread = true;
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}
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InductionThread::~InductionThread()
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{
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m_runThread = false;
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std::this_thread::sleep_for(std::chrono::seconds(2));
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SAFE_DELETE(m_VasopressinBolus);
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SAFE_DELETE(m_ringers);
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SAFE_DELETE(m_blood);
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SAFE_DELETE(m_plasma);
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SAFE_DELETE(m_platelet);
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}
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void InductionThread::AdministerVasopressin(double& bolus)
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{
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m_VasopressinBolus->SetAdminRoute(CDM::enumBolusAdministration::Intravenous);
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m_VasopressinBolus->GetConcentration().SetValue(1.0, MassPerVolumeUnit::mg_Per_mL);
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m_VasopressinBolus->GetDose().SetValue(bolus, VolumeUnit::mL);
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m_mutex.lock();
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m_bg->ProcessAction(*m_VasopressinBolus);
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m_mutex.unlock();
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}
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void InductionThread::SetRingersInfusionRate(double& volume, double& rate)
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{
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m_ringers->GetBagVolume().SetValue(volume, VolumeUnit::mL);
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m_ringers->GetRate().SetValue(rate, VolumePerTimeUnit::mL_Per_hr);
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m_ivBagVolume_mL = volume;
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m_mutex.lock();
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m_bg->ProcessAction(*m_ringers);
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m_mutex.unlock();
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}
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void InductionThread::SetBloodInfusionRate(double& volume, double& rate)
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{
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m_blood->GetBagVolume().SetValue(volume, VolumeUnit::mL);
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m_blood->GetRate().SetValue(rate, VolumePerTimeUnit::mL_Per_hr);
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m_ivBagVolumeBlood_mL = volume;
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m_mutex.lock();
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m_bg->ProcessAction(*m_blood);
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m_mutex.unlock();
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}
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void InductionThread::SetPlasmaInfusionRate(double& volume, double& rate)
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{
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m_plasma->GetBagVolume().SetValue(volume, VolumeUnit::mL);
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m_plasma->GetRate().SetValue(rate, VolumePerTimeUnit::mL_Per_min);
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m_ivBagVolumePlasma_mL = volume;
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m_mutex.lock();
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m_bg->ProcessAction(*m_plasma);
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m_mutex.unlock();
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}
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void InductionThread::SetPlateletInfusionRate(double& volume, double& rate)
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{
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m_platelet->GetBagVolume().SetValue(volume, VolumeUnit::mL);
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m_platelet->GetRate().SetValue(rate, VolumePerTimeUnit::mL_Per_hr);
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m_ivBagVolumePlatelet_mL = volume;
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m_mutex.lock();
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m_bg->ProcessAction(*m_blood);
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m_mutex.unlock();
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}
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void InductionThread::AdvanceTimeFluids()
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{
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m_mutex.lock();
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m_bg->AdvanceModelTime(1.0, TimeUnit::s);
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if (m_blood->HasBagVolume() && m_blood->HasRate()) {
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m_TotalVolume_mL += (m_blood->GetRate().GetValue(VolumePerTimeUnit::mL_Per_s));
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m_TotalVolumeBlood_mL += (m_blood->GetRate().GetValue(VolumePerTimeUnit::mL_Per_s));
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m_ivBagVolumeBlood_mL += (-m_blood->GetRate().GetValue(VolumePerTimeUnit::mL_Per_s));
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if (m_ivBagVolumeBlood_mL < 0.0) {
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m_bg->GetLogger()->Info("blood bag is empty \n");
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m_ivBagVolumeBlood_mL = 0.0;
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m_blood->Clear();
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}
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}
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//repeat for plasma
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if (m_plasma->HasBagVolume() && m_plasma->HasRate()) {
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m_TotalVolume_mL += (m_plasma->GetRate().GetValue(VolumePerTimeUnit::mL_Per_s));
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m_TotalVolumePlasma_mL += (m_plasma->GetRate().GetValue(VolumePerTimeUnit::mL_Per_s));
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m_ivBagVolumePlasma_mL += (-m_plasma->GetRate().GetValue(VolumePerTimeUnit::mL_Per_s));
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if (m_ivBagVolumePlasma_mL < 0.0) {
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m_bg->GetLogger()->Info("blood bag is empty \n");
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m_ivBagVolumePlasma_mL = 0.0;
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m_plasma->Clear();
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}
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}
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m_bg->GetEngineTrack()->GetDataTrack().Probe("totalFluid_mL", m_TotalVolume_mL);
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m_bg->GetEngineTrack()->GetDataTrack().Probe("bagVolume_mL", m_ivBagVolume_mL);
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m_bg->GetEngineTrack()->GetDataTrack().Probe("totalFluidBlood_mL", m_TotalVolumeBlood_mL);
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m_bg->GetEngineTrack()->GetDataTrack().Probe("bagVolumeBlood_mL", m_ivBagVolumeBlood_mL);
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m_bg->GetEngineTrack()->GetDataTrack().Probe("totalFluidPlasma_mL", m_TotalVolumePlasma_mL);
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m_bg->GetEngineTrack()->GetDataTrack().Probe("bagVolumePlasma_mL", m_ivBagVolumePlasma_mL);
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m_bg->GetEngineTrack()->TrackData(m_bg->GetSimulationTime(TimeUnit::s));
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m_mutex.unlock();
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std::this_thread::sleep_for(std::chrono::milliseconds(25));
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}
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void InductionThread::Status()
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{
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m_mutex.lock();
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m_bg->GetLogger()->Info(asprintf("The patient suffered a hemorrhage wound %f %s", m_bg->GetSimulationTime(TimeUnit::min), " min ago"));
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m_bg->GetLogger()->Info(asprintf("Tidal Volume : %f %s", m_bg->GetRespiratorySystem()->GetTidalVolume(VolumeUnit::mL), "mL"));
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m_bg->GetLogger()->Info(asprintf("Systolic Pressure : %f %s", m_bg->GetCardiovascularSystem()->GetSystolicArterialPressure(PressureUnit::mmHg), "mmHg"));
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m_bg->GetLogger()->Info(asprintf("Diastolic Pressure : %f %s", m_bg->GetCardiovascularSystem()->GetDiastolicArterialPressure(PressureUnit::mmHg), "mmHg"));
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m_bg->GetLogger()->Info(asprintf("Heart Rate : %f %s", m_bg->GetCardiovascularSystem()->GetHeartRate(FrequencyUnit::Per_min), "bpm"));
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m_bg->GetLogger()->Info(asprintf("Respiration Rate : %f %s", m_bg->GetRespiratorySystem()->GetRespirationRate(FrequencyUnit::Per_min), "bpm"));
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m_bg->GetLogger()->Info(asprintf("Oxygen Saturation : %f", m_bg->GetBloodChemistrySystem()->GetOxygenSaturation()));
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m_bg->GetLogger()->Info(asprintf("Blood Volume: %f %s", m_bg->GetCardiovascularSystem()->GetBloodVolume(VolumeUnit::mL), "mL"));
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m_bg->GetLogger()->Info(asprintf("Systemic Vascular Resistance : %f %s", m_bg->GetCardiovascularSystem()->GetSystemicVascularResistance(FlowResistanceUnit::mmHg_s_Per_mL), "mmHg_s_Per_mL"));
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m_bg->GetLogger()->Info(asprintf("Mean Urine Output : %f %s", m_bg->GetRenalSystem()->GetMeanUrineOutput(VolumePerTimeUnit::mL_Per_hr), "mL_Per_hr"));
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if (m_ringers->HasBagVolume()) {
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m_bg->GetLogger()->Info(asprintf("Remaining blood Volume in bag: %f %s", m_ivBagVolumeBlood_mL, "mL"));
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}
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std::cout << std::endl;
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m_mutex.unlock();
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}
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void AdministerInduction();
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{
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const SEPatient& patient = m_bg->GetPatient();
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double weight_kg = patient.GetWeight(MassUnit::kg);
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}
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//routine to administer fluids with a goal directed therapy for urine ourput
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void InductionThread::FluidLoading()
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{
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//redblood cell unit volume:
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double pRBCVolume_mL = 350;
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//plasma unit volume
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double plasmaVolume_mL = 200;
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//platlet volume
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double platletVolume_mL = 300;
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//rates:
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double bloodRate_mL_Per_hr = 250;
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double plasmaRate_mL_Per_min = 15;
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//we will activate the protocol when shock index reaches 1:
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double shockIndex = 0.0;
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//shock index requires the heart rate and the systolic pressure:
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double heartRate_min = m_bg->GetCardiovascularSystem()->GetHeartRate(FrequencyUnit::Per_min);
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double systolicPressure_mmHg = m_bg->GetCardiovascularSystem()->GetSystolicArterialPressure(PressureUnit::mmHg);
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//update shock index:
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shockIndex = heartRate_min / systolicPressure_mmHg;
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//time keeping
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int checkTime_s = 3600;
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int LabTime_s = 1800; // 60 mins
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double volume = 0.0;
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//how long do we want to run for?
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double maxSimTime_hr = 2.0;
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double hemTime_min = 20.0;
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//compute urine production and max fluid requirements, per parkland formula
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const SEPatient& patient = m_bg->GetPatient();
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double weight_kg = patient.GetWeight(MassUnit::kg);
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double initialInfustion_mL_Per_hr = 0.0; //tbsa * 10.0; // Should start at 10*tbsa // (DayLimit_mL / 0.5) / 8.0; //half of the fluid should be loaded in the first 8 hours;
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double initialInfustionAlbumin_mL_Per_hr = 50.0; //tbsa * 10.0; // Should start at 10*tbsa // (DayLimit_mL / 0.5) / 8.0; //half of the fluid should be loaded in the first 8 hours;
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double temp = 0.0;
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bool Labs = true;
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bool fluidOn = false;
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m_bg->GetLogger()->Info(asprintf("Beginning care"));
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while (m_runThread) {
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//pull the data
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//check for bleeding intervention:
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if (m_bg->GetSimulationTime(TimeUnit::min) > hemTime_min && m_hemorrhage->GetInitialRate().GetValue(VolumePerTimeUnit::mL_Per_min) > ZERO_APPROX) {
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m_hemorrhage->GetInitialRate().SetValue(0, VolumePerTimeUnit::mL_Per_min);
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m_bg->ProcessAction(*m_hemorrhage);
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}
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heartRate_min = m_bg->GetCardiovascularSystem()->GetHeartRate(FrequencyUnit::Per_min);
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systolicPressure_mmHg = m_bg->GetCardiovascularSystem()->GetSystolicArterialPressure(PressureUnit::mmHg);
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shockIndex = heartRate_min / systolicPressure_mmHg;
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if (shockIndex >= 1.0) {
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fluidOn = true;
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}
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//initial fluids:
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if (fluidOn && m_ivBagVolumeBlood_mL == 0.0 && m_ivBagVolumePlasma_mL == 0.0) {
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//set 1:1 fluid infusion:
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SetPlasmaInfusionRate(plasmaVolume_mL, plasmaRate_mL_Per_min);
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SetBloodInfusionRate(pRBCVolume_mL, bloodRate_mL_Per_hr);
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m_bg->GetLogger()->Info(asprintf("Beginning Intervention with infusion at %f %s", bloodRate_mL_Per_hr, "mL_Per_hr"));
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}
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// Generate blood gas amount of time
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if (((int)m_bg->GetSimulationTime(TimeUnit::s) + 1) % LabTime_s == 0 && Labs == true) {
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//run our blood gas assesment every hour:
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m_bg->GetPatientAssessment(bga);
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m_bg->GetLogger()->Info(asprintf("Checked blood/gas Labs"));
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}
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//check status every hour, reset the volume while we are at it
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if (((int)m_bg->GetSimulationTime(TimeUnit::s) + 1) % checkTime_s == 0) {
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Status();
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}
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// make sure that the bag is full
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if (m_ivBagVolumeBlood_mL < 1.0 && fluidOn) {
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m_blood->GetBagVolume().SetValue(pRBCVolume_mL, VolumeUnit::mL);
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m_bg->GetLogger()->Info("blood IV bag is low, refilling bag \n");
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m_bg->ProcessAction(*m_blood);
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m_ivBagVolumeBlood_mL = pRBCVolume_mL; //tracking purposes
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}
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// make sure that the plasma bag is full
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if (m_ivBagVolumePlasma_mL < 1.0 && fluidOn) {
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m_plasma->GetBagVolume().SetValue(plasmaVolume_mL, VolumeUnit::mL);
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m_bg->GetLogger()->Info("blood IV bag is low, refilling bag \n");
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m_bg->ProcessAction(*m_blood);
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m_ivBagVolumePlasma_mL = plasmaVolume_mL; //tracking purposes
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}
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//exit checks:
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if (m_bg->GetPatient().IsEventActive(CDM::enumPatientEvent::IrreversibleState)) {
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//m_bg->GetLogger()->Info(std::stringstream() << "oh no!");
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m_bg->GetLogger()->Info("///////////////////////////////////////////////////////////////");
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m_runThread = false;
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}
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if (m_bg->GetSimulationTime(TimeUnit::hr) > maxSimTime_hr) {
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m_bg->GetLogger()->Info("This simulation has gone on too long");
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m_runThread = false;
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}
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//advance time
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AdvanceTime();
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}
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}
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