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Commit 737e41ee authored by Aaron Bray's avatar Aaron Bray
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Merge branch '3.x' into study/hydrocephalus 

#Additionts
#            Refactor PulseConfiguration to move SubMgr from ctor to Serialize methods

# Conflicts:
#	.gitignore
parents 26082f87 ae5b93d1
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.gitignore
View file @ 737e41ee
......@@ -9,12 +9,10 @@
src/schema/schema_last_built
/src/cpp/bind
/src/csharp/pulse/bind
/src/java/com
/src/java/pulse/cdm/bind
/src/java/pulse/cpm/bind
/src/java/pulse/study/bind/hydrocephalus
/src/java/pulse/study/bind/multiplex_ventilation
/src/java/pulse/study/bind/sensitivity_analysis
/src/java/com/google
/src/java/com/kitware/pulse/cdm/bind
/src/java/com/kitware/pulse/cpm/bind
/src/java/com/kitware/pulse/study/bind
/src/python/pulse/cdm/bind
/src/python/pulse/cpm/bind
/src/python/pulse/study/bind
......
NOTICE
View file @ 737e41ee
......@@ -61,18 +61,6 @@ Licensed under BSD 3-clause
https://opensource.org/licenses/BSD-3-Clause
------------------------------------------------------------------------------
This product uses the log4cpp package
http://log4cpp.sourceforge.net/
Licensed under the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
https://www.gnu.org/licenses/lgpl.html
------------------------------------------------------------------------------
When on Windows machines, this product uses the dirent.h package
......@@ -105,3 +93,41 @@ SOFTWARE.
------------------------------------------------------------------------------
When building Python API support, this product uses the pybind11 package
https://github.com/pybind/pybind11
Licensed under the under the following:
Copyright (c) 2016 Wenzel Jakob <wenzel.jakob@epfl.ch>, All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of the copyright holder nor the names of its contributors
may be used to endorse or promote products derived from this software
without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Please also refer to the file CONTRIBUTING.md, which clarifies licensing of
external contributions to this project including patches, pull requests, etc.
------------------------------------------------------------------------------
\ No newline at end of file
bin/EngineState.json
View file @ 737e41ee
{
"Name":"BasicStandard",
"Description":"Basic scenario measuring patient vitals with no insults or interventions",
"EngineStateFile":"./states/StandardMale@0s.json",
"EngineStateFile":"./states/StandardMale@0s.pbb",
"DataRequestManager": {"DataRequest":[
{"DecimalFormat":{"Precision":1},"Category":"Patient", "PropertyName":"Weight", "Unit":"kg"},
......
bin/InitialPatientState.json
View file @ 737e41ee
......@@ -3,12 +3,13 @@
"Name": "InitialStableState",
"Description": "Stabilize a patient and save out the engines state at time zero",
"PatientConfiguration": { "PatientFile": "StandardMale.json" },
"AnyAction": [{
"Serialize": {
}
"AnyAction":
[{
"Serialize": { "Type": "Save" }
}]
},
"Configuration": {
"Configuration":
{
"WritePatientBaselineFile": "On"
}
}
bin/run.cmake.in
View file @ 737e41ee
# Scripts to assist developers
# Mostly these are calling the test suite driver and validator classes in Java
# TODO More Test Targets
# Rebasing
# com.kitware.physiology.utilities.testing.Rebase [from to (config|ALL)]
#
# Ploting
# com.kitware.physiology.utilities.csv.plots.PlotDriver
#
# Reconfigure the config file (in memory) so we can test serialization
# com.kitware.physiology.utilities.testing.Reconfiguration
find_package(Java REQUIRED)
include(UseJava)
......@@ -23,24 +14,19 @@ endif()
#set(Java_JAVA_EXECUTABLE "/the_jdk_I_want/bin/java)
set(JAVA_CLASSPATH Pulse.jar
"@CMAKE_SOURCE_DIR@/src/java/jar/javassist-3.16.1-GA.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/jcommon-1.0.16.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/jdom-2.0.2.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/jfreechart-1.0.13.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/gson-2.8.5.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/guava-26.0-jre.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/log4j-1.2.17.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-3.13-20150929.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-ooxml-3.13-20150929.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-ooxml-schemas-3.13-20150929.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/pdfbox-2.0.0-RC3.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/reflections-0.9.9-RC1-uberjar.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/xmlbeans-2.6.0.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/zip4j-1.3.1.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/org.eclipse.jgit-4.11.0.201803080745-r.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/slf4j-api-1.7.25.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/slf4j-simple-1.7.25.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/error_prone_annotations-2.3.2.jar")
"@CMAKE_SOURCE_DIR@/src/java/jar/commons-collections4-4.4.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/commons-compress-1.19.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/commons-math3-3.6.1.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/error_prone_annotations-2.3.4.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/gson-2.8.6.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/guava-29.0-jre.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/jfreechart-1.5.0.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/javassist.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-4.1.2.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-ooxml-4.1.2.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/poi-ooxml-schemas-4.1.2.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/reflections-0.9.12.jar"
"@CMAKE_SOURCE_DIR@/src/java/jar/xmlbeans-3.1.0.jar")
if(NOT WIN32)
string(REPLACE ";" ":" JAVA_CLASSPATH "${JAVA_CLASSPATH}")
......@@ -48,22 +34,22 @@ endif()
if(TYPE STREQUAL "tests" OR TYPE STREQUAL "SystemValidation" OR TYPE STREQUAL "PatientValidation")
if(TYPE STREQUAL "tests")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver CDMUnitTests.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver EngineUnitTests.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver ScenarioVerification.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver CDMUnitTests.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver EngineUnitTests.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver ScenarioVerification.config)
endif()
if(TYPE STREQUAL "SystemValidation" OR TYPE STREQUAL "tests")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver SystemVerification.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.validation.SystemValidation TEST)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver SystemVerification.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.validation.SystemValidation TEST)
endif()
if(TYPE STREQUAL "PatientValidation" OR TYPE STREQUAL "tests")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver PatientVerification.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.validation.PatientValidation TEST)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver PatientVerification.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.validation.PatientValidation TEST)
endif()
elseif(TYPE STREQUAL "genData")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.dataset.DataSetReader)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.dataset.DataSetReader)
elseif(TYPE STREQUAL "genStates")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver InitialPatientStates.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver InitialPatientStates.config)
elseif(TYPE STREQUAL "doxygen")
file(READ @CMAKE_SOURCE_DIR@/docs/Doxygen/header.html HEADER)
file(READ @CMAKE_SOURCE_DIR@/docs/Doxygen/footer.html FOOTER)
......@@ -90,13 +76,13 @@ elseif(TYPE STREQUAL "doxygen")
file(WRITE @CMAKE_SOURCE_DIR@/docs/Doxygen/panel_footer.html "${FOOTER_PANEL}")
file(APPEND @CMAKE_SOURCE_DIR@/docs/Doxygen/panel_footer.html "${FOOTER}")
# These are run above
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.validation.SystemValidation BASELINE)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.validation.PatientValidation BASELINE)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.doxygen.DoxygenPreprocessor "@CMAKE_SOURCE_DIR@/docs/Markdown" ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.doxygen.DoxygenPreprocessor "@CMAKE_SOURCE_DIR@/docs/Methodology" ./docs/markdown ./test_results/tables)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.doxygen.Proto2Doxygen "@CMAKE_SOURCE_DIR@/src/schema" ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.doxygen.CDM2MD ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.utilities.csv.plots.PlotDriver PlotRun.config)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.validation.SystemValidation BASELINE)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.validation.PatientValidation BASELINE)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.doxygen.DoxygenPreprocessor "@CMAKE_SOURCE_DIR@/docs/Markdown" ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.doxygen.DoxygenPreprocessor "@CMAKE_SOURCE_DIR@/docs/Methodology" ./docs/markdown ./test_results/tables)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.doxygen.Proto2Doxygen "@CMAKE_SOURCE_DIR@/src/schema" ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.doxygen.CDM2MD ./docs/markdown)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.utilities.csv.plots.PlotDriver PlotRun.config)
execute_process(COMMAND doxygen ./docs/full.doxy)
# Build our landing files
setup_landing_page(index.html)
......@@ -112,12 +98,30 @@ elseif(TYPE STREQUAL "protoc")
-P "@CMAKE_SOURCE_DIR@/src/schema/GenerateBindings.cmake")
elseif(TYPE STREQUAL "updateBaselines")
execute_process(COMMAND ${CMAKE_COMMAND} --build "@CMAKE_CURRENT_BINARY_DIR@" --target UpdateVerification)
elseif(TYPE STREQUAL "jar")
execute_process(COMMAND ${CMAKE_COMMAND} --build "@CMAKE_CURRENT_BINARY_DIR@" --target PulseJava)
elseif(TYPE STREQUAL "rebase")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.Rebase)
# find Git and if available set GIT_HASH variable
find_package(Git QUIET)
if(GIT_FOUND)
execute_process(
COMMAND ${GIT_EXECUTABLE} log -1 --pretty=format:%h
OUTPUT_VARIABLE GIT_HASH
OUTPUT_STRIP_TRAILING_WHITESPACE
ERROR_QUIET
WORKING_DIRECTORY
@CMAKE_SOURCE_DIR@
)
endif()
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.Rebase ${GIT_HASH})
elseif(TYPE STREQUAL "FullReport")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SEReportResults)
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SEReportResults)
elseif(TYPE STREQUAL "plotter")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.utilities.csv.plots.CSVPlotTool ${ARG1})
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.utilities.csv.plots.CSVPlotTool ${ARG1})
else()
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" pulse.cdm.testing.SETestDriver ${TYPE}.config)
if(${TYPE} MATCHES "Plot")
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.utilities.csv.plots.PlotDriver ${TYPE}.config)
else()
execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.cdm.testing.SETestDriver ${TYPE}.config)
endif()
endif()
data/config/CDMUnitTests.config
View file @ 737e41ee
......@@ -14,7 +14,7 @@ PlotResults=true
PercentDifference=2.0
Threads=-1
Executor=pulse.cdm.testing.CDMUnitTestDriver
Executor=com.kitware.pulse.cdm.testing.CDMUnitTestDriver
Macro CDMUnitTest=CDMUnitTestDriver FastPlotErrors Baseline=unit_tests/cdm/ Computed=./test_results/unit_tests/cdm/
@group Simple Circuits
......
data/config/DebugPlots.config
View file @ 737e41ee
......@@ -17,7 +17,9 @@
# ImageDimensions - Specify the image width and height in pixels (i.e. ImageDimesions=1600,800) Default is 1600x800, but ActionEventPlots can stretch automatically
# RemoveLegends - Removes all legends from the generated plot
# FontSize - Set the font size of axis labels and chart title (FontSize=22 by default)
# LegendFontSize - Set the font size of the legend (LegendFontSize=15 by default)
# OutputFilename - Set the desired filename for the generated plot (no spaces allowed; will default to the chart title if nothing is set for this)
# PercentOfBaseline - All values will be set to Value@TimeX / Values@Time0
#FLAGS FOR ACTIONEVENTPLOTTER ONLY
# Header - Specify the header(s) that you want to plot on the Y axis
......@@ -47,14 +49,18 @@
# FLAGS FOR RESPIRATORY PFT PLOTTER ONLY
# PFTFile - Specify the path and filename for the .pba containing the PFT data you want to plot (No spaces allowed)
Plotter=pulse.utilities.csv.plots.ActionEventPlotter
Plotter=pulse.utilities.csv.plots.MultiPlotter
Plotter=pulse.utilities.csv.plots.ConvexHullPlotter
Plotter=pulse.utilities.csv.plots.RespiratoryPFTPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.ActionEventPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.MultiPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.ConvexHullPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.RespiratoryPFTPlotter
Plotter=com.kitware.pulse.utilities.csv.plots.MultiSourcePlotter
#ScenarioName=PlotterType Flag1=Stuff Flag2=Stuff Flag3 FlagN
#PralidoximeValidation=ActionEventPlotter Title=Pralidoxime NoActions NoEvents LogAxis Header=Pralidoxime-PlasmaConcentration(ug/L) DataPathOverride=./Scenarios/Validation/ DataFileOverride=PralidoximeValidationResults.csv ExperimentalData=../docs/Validation/Pharmacokinetic/CSVs/Pralidoxime.csv OutputOverride=..\docs\Doxygen\html\plots\Drugs
#VentricularSystolicDysfunction=ActionEventPlotter NoGrid Title=None Header=BloodVolume(L) OutputOverride=./docs/html/plots/Cardiovascular OutputFilename=HeartFailure.jpg
CardiacShock=MultiPlotter X1Label=Percent_Of_Blood_Loss X1=BloodVolume(L) Y1=CardiacOutput(L/min) Y1LowerBound=0 X2=BloodVolume(L) Y2=MeanArterialPressure(mmHg) Y2LowerBound=0 X1LowerBound=0 X1UpperBound=0.5 DataPathVerificationOverride=scenarios/patient/ Title=None DataFileOverride=HemorrhageClass4NoFluidResults.csv OutputOverride=./docs/html/plots/Cardiovascular OutputFilename=CardiacShock.jpg
#RespiratoryValidation=RespiratoryPFTPlotter Header=TotalLungVolume(mL) VerificationDir=validation/systems/ PFTFile=RespiratoryValidationPFT@120.02s.json Title=Pulmonary_Function_Test_Results OutputOverride=./docs/html/plots/Respiratory/
CardiacShock=MultiPlotter Title=Cardiovascular_Response_To_Hemorrhage PercentOfBaseline X1Label=Percent_Of_Blood_Loss X1=BloodVolume(L) Y1=CardiacOutput(L/min) Y1LowerBound=0 X2=BloodVolume(L) Y2=MeanArterialPressure(mmHg) Y2LowerBound=0 X1LowerBound=0 X1UpperBound=50 DataPathVerificationOverride=scenarios/patient/ Title=None DataFileOverride=HemorrhageClass4NoFluidResults.csv OutputOverride=./docs/html/plots/Cardiovascular OutputFilename=CardiacShock.jpg
HemorrhageGroups=MultiSourcePlotter Title=Cardiovascular_Hemorrhage_Groups PercentOfBaseline X1=Time(s) Y1=MeanArterialPressure(mmHg) Y1Label=Mean_Arterial_Pressure_Delta Y1LowerBound=0 Y1UpperBound=100 DataPathVerificationOverride=scenarios/patient/ Title=None DataFileOverride=HemorrhageGroup1Results.csv,HemorrhageGroup2Results.csv,HemorrhageGroup3Results.csv,HemorrhageGroup4Results.csv,HemorrhageGroup5Results.csv,HemorrhageGroup6Results.csv OutputOverride=./docs/html/plots/Cardiovascular OutputFilename=HemorrhageGroups.jpg
HemorrhageClass3NoFluid=ActionEventPlotter LegendOnly ActionsOnly Header=RightAfferentArterioleResistance(mmHg_min/mL) Title=HemorrhageClass4NoFluidLegend VerificationDir=patient OutputOverride=./docs/html/plots/Renal/ NoEvents ImageDimensions=1500,160
data/config/DebugRun.config
View file @ 737e41ee
......@@ -22,9 +22,9 @@ Threads=-1
# Time stamp periods is creating a file per save and using the time stamp as naming convention
#AutoSerialization=./states/testing/,5,On,On,On
Executor=pulse.cdm.testing.CDMUnitTestDriver
Executor=pulse.engine.testing.EngineUnitTestDriver
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.cdm.testing.CDMUnitTestDriver
Executor=com.kitware.pulse.engine.testing.EngineUnitTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro CDMUnitTest=CDMUnitTestDriver FastPlotErrors Baseline=unit_tests/cdm/ Computed=./test_results/unit_tests/cdm
Macro EngineUnitTest=EngineUnitTestDriver FastPlot Baseline=unit_tests/pulse/ Computed=./test_results/unit_tests/pulse
......
data/config/DrugPKVerification.config
View file @ 737e41ee
......@@ -20,7 +20,7 @@ Threads=-1
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
......
data/config/EngineUnitTests.config
View file @ 737e41ee
......@@ -14,7 +14,7 @@ PlotResults=true
PercentDifference=2.0
Threads=-1
Executor=pulse.engine.testing.EngineUnitTestDriver
Executor=com.kitware.pulse.engine.testing.EngineUnitTestDriver
Macro EngineUnitTest=EngineUnitTestDriver FastPlotErrors Baseline=unit_tests/pulse/ Computed=./test_results/unit_tests/pulse/
Macro FullPlotEngineUnitTest=EngineUnitTestDriver FullPlotErrors Baseline=unit_tests/pulse/ Computed=./test_results/unit_tests/pulse/
......@@ -45,6 +45,10 @@ RespiratoryDriver = EngineUnitTest Results=RespiratoryDriverOutput
AnesthesiaMachineCircuitAndTransport = EngineUnitTest Results=AnesthesiaMachineCircuitOutput,AnesthesiaMachineTransportOutput
RespiratoryWithAnesthesiaMachineCircuitAndTransport = EngineUnitTest Results=RespiratoryAndAnesthesiaMachineCircuitOutput,RespiratoryAndAnesthesiaMachineTransportOutput
@group MechanicalVentilator
MechanicalVentilatorCircuitAndTransport = EngineUnitTest Results=MechanicalVentilatorCircuitOutput,MechanicalVentilatorTransportOutput
RespiratoryWithMechanicalVentilatorCircuitAndTransport = EngineUnitTest Results=RespiratoryAndMechanicalVentilatorCircuitOutput,RespiratoryAndMechanicalVentilatorTransportOutput
@group Inhaler
RespiratoryWithInhalerCircuitAndTransport = EngineUnitTest Results=RespiratoryAndInhalerCircuitOutput,RespiratoryAndInhalerTransportOutput,AerosolInhalerTransportOutput
......
data/config/InitialPatientStates.config
View file @ 737e41ee
......@@ -16,7 +16,7 @@ Patients=all
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioRun=ScenarioTestDriver NoPlot Scenario=./ Computed=./test_results/scenarios/
......
data/config/LongVerificationScenarios.config
View file @ 737e41ee
......@@ -22,7 +22,7 @@ Threads=-1
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
......
data/config/PatientVerification.config
View file @ 737e41ee
......@@ -16,7 +16,7 @@ Patients=all
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
......
data/config/PlotRun.config
View file @ 737e41ee
This diff is collapsed.
data/config/Rebase.config
View file @ 737e41ee
......@@ -3,8 +3,8 @@ DebugRun.config
#CDMUnitTests.config
#EngineUnitTests.config
#LongVerificationScenarios.config
DrugPKVerification.config
PatientVerification.config
SystemVerification.config
ScenarioVerification.config
#DrugPKVerification.config
#PatientVerification.config
#SystemVerification.config
#ScenarioVerification.config
data/config/ScenarioVerification.config
View file @ 737e41ee
......@@ -22,7 +22,7 @@ Threads=-1
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
......@@ -129,6 +129,11 @@ equipment/NasalCannula.json = ScenarioTest
equipment/NonRebreatherMask.json = ScenarioTest
equipment/SimpleMask.json = ScenarioTest
@group Nutrition
nutrition/Nutrition.json = ScenarioTest
nutrition/SodiumIngestion.json = ScenarioTest
nutrition/WaterIngestion.json = ScenarioTest
@group Drugs
drug/Albuterol.json = ScenarioTest
drug/Desflurane.json = ScenarioTest
......@@ -172,13 +177,13 @@ miscellaneous/ImpairedAlveolarExchangeFraction.json = ScenarioTest
miscellaneous/ImpairedAlveolarExchangeSeverity.json = ScenarioTest
miscellaneous/ImpairedAlveolarExchangeSurfaceArea.json = ScenarioTest
miscellaneous/MultiDrug.json = ScenarioTest
miscellaneous/Nutrition.json = ScenarioTest
miscellaneous/PulmonaryShunt.json = ScenarioTest
miscellaneous/SpirometryComparison.json = ScenarioTest
miscellaneous/SpirometryHealthy.json = ScenarioTest
miscellaneous/SpirometryPulmonaryFibrosis.json = ScenarioTest
miscellaneous/TBIandDrugs.json = ScenarioTest
@group Compartments
#compartments/UserSpecific.json = ScenarioTest
compartments/AnesthesiaMachineCompartments.json = ScenarioTest
......
data/config/SystemVerification.config
View file @ 737e41ee
......@@ -16,7 +16,7 @@ Threads=-1
# AutoSerialize = Directory,Period(in seconds, 0 turns off constant saving),TimeStampPeriods,AfterActions,Reload
#AutoSerialization=./states/testing/,5,Off,On,On
Executor=pulse.engine.testing.ScenarioTestDriver
Executor=com.kitware.pulse.engine.testing.ScenarioTestDriver
Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
......
data/human/adult/baselines/scenarios/compartments/PulmonaryCompartments.zip.sha512
View file @ 737e41ee
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\ No newline at end of file
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\ No newline at end of file
data/human/adult/baselines/scenarios/drug/Albuterol.zip.sha512
View file @ 737e41ee
c17b36bd48052b730ef5523b5531ac11f85704bc44e069965837a31f26f0cf33994ece8cb303e70f73f25cddfa11493f6674fceb3d43cbe2497112290acdcfdc
\ No newline at end of file
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\ No newline at end of file
data/human/adult/baselines/scenarios/energyenvironment/FireFighter.zip.sha512
View file @ 737e41ee
312ccd1894b864f5edd87d0ab4c3075fc6e5003a535967b5abfd741a1d062ac6b6b268a65a597039ca39a3974e1bf3065d4876c12cea3eb27961900d299b72ce
\ No newline at end of file
0118dc9e95faaa371b9d0448832373df9324881fdd5b5634250477fa9558a3db27fa2a62a8390d324e75395b5281fea942d30eb61eab0855a56e3fa3d39c492a
\ No newline at end of file
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