Merge branch '3.x'

CMakeLists.txt

@@ -77,7 +77,7 @@ if(${PROJECT_NAME}_SUPERBUILD)
     option(USE_SYSTEM_${extProj} "Exclude ${extProj} from superbuild and use an existing build." OFF)
     mark_as_advanced(USE_SYSTEM_${extProj})
   endmacro()
-  
+
   define_dependency(Eigen3)
   if(WIN32)
     # *nix systems have this already
@@ -92,7 +92,7 @@ if(${PROJECT_NAME}_SUPERBUILD)
         message(FATAL_ERROR "Unable to support Python API, cannot find Python3")
     endif()
   endif()
-  
+
   if(${PROJECT_NAME}_DEPENDENCIES)
     if(MSVC OR XCode)
       if(NOT ${PROJECT_NAME}_SLAVE_BUILD)
@@ -122,7 +122,7 @@ endif()
 #                               INNERBUILD
 #-----------------------------------------------------------------------------
 
-if(MSVC)  
+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)
@@ -153,19 +153,29 @@ if(WIN32)
   # *nix systems have this already
   find_package(Dirent REQUIRED)
 endif()
-# Use the config written by protobuf
-set(protobuf_MODULE_COMPATIBLE ON CACHE BOOL "" FORCE)
-find_package(protobuf REQUIRED NO_DEFAULT_PATH)
+
+# Tell protobuf-config.cmake to try to be compatible with FindProtobuf.cmake;
+# this makes it easier for us to work with either one
+set(protobuf_MODULE_COMPATIBLE ON CACHE BOOL "CMake built-in FindProtobuf.cmake module compatible" FORCE)
+mark_as_advanced(protobuf_MODULE_COMPATIBLE)
+
+# Try to use the config written by protobuf
+find_package(protobuf QUIET CONFIG NO_DEFAULT_PATH)
+if(protobuf_DIR AND protobuf_FOUND)
+  # Success; set flag so we will reexport protobuf for our users
+  set(Pulse_USING_PROTOBUF_DIR ON)
+elseif(NOT protobuf_FOUND)
+  # Nope; fall back on FindProtobuf.cmake
+  find_package(Protobuf REQUIRED)
+endif()
+
+# Ensure protobuf exported target exists
 get_target_property(PROTOBUF_LIBRARY_RELEASE protobuf::libprotobuf LOCATION_RELEASE)
 get_target_property(PROTOBUF_LIBRARY_DEBUG protobuf::libprotobuf LOCATION_DEBUG)
-#message(STATUS "PROTOBUF_LIBRARY_RELEASE ${PROTOBUF_LIBRARY_RELEASE}")
-#message(STATUS "PROTOBUF_LIBRARY_DEBUG ${PROTOBUF_LIBRARY_DEBUG}")
 install(FILES ${PROTOBUF_LIBRARY_RELEASE} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib OPTIONAL)
 install(FILES ${PROTOBUF_LIBRARY_DEBUG} DESTINATION ${CMAKE_INSTALL_PREFIX}/lib OPTIONAL)
 get_filename_component(PROTOBUF_LIBRARY_DEBUG ${PROTOBUF_LIBRARY_DEBUG} NAME)
 get_filename_component(PROTOBUF_LIBRARY_RELEASE ${PROTOBUF_LIBRARY_RELEASE} NAME)
-#message(STATUS "PROTOBUF_LIBRARY_RELEASE ${PROTOBUF_LIBRARY_RELEASE}")
-#message(STATUS "PROTOBUF_LIBRARY_DEBUG ${PROTOBUF_LIBRARY_DEBUG}")
 
 set(SCHEMA_SRC "${CMAKE_SOURCE_DIR}/schema")
 set(SCHEMA_DST "${CMAKE_SOURCE_DIR}/schema/bind")
@@ -228,7 +238,7 @@ export(
 # Configure '${PROJECT_NAME}Config.cmake' for a build tree
 set(build_config ${CMAKE_BINARY_DIR}/${PROJECT_NAME}Config.cmake)
 configure_package_config_file(
-  cmake/${PROJECT_NAME}Config.cmake.in 
+  cmake/${PROJECT_NAME}ConfigBuild.cmake.in
   ${build_config}
   INSTALL_DESTINATION "${PROJECT_BINARY_DIR}"
   )
@@ -244,7 +254,7 @@ install(
 
 set(install_config ${PROJECT_BINARY_DIR}/CMakeFiles/${PROJECT_NAME}Config.cmake)
 configure_package_config_file(
-  cmake/${PROJECT_NAME}Config.cmake.in 
+  cmake/${PROJECT_NAME}ConfigInstall.cmake.in
   ${install_config}
   INSTALL_DESTINATION ${${PROJECT_NAME}_INSTALL_CONFIG_DIR}
   )

bin/run.bat

 :: Refer to the Running and Testing Section in the ReadMe.md for %1 options
 
-cmake -DTYPE:STRING=%1 -DARG1:STRING=%2 -P run.cmake
\ No newline at end of file
+cmake -DTYPE:STRING=%1 -DARG1:STRING=%2 -DARG2:STRING=%3 -P run.cmake
\ No newline at end of file

bin/run.cmake.in

@@ -98,9 +98,9 @@ elseif(TYPE STREQUAL "protoc")
                                            -DPulse_PYTHON_API:BOOL=@Pulse_PYTHON_API@
                                            -P "@CMAKE_SOURCE_DIR@/src/schema/GenerateBindings.cmake")
 elseif(TYPE STREQUAL "updateBaselines")
-  execute_process(COMMAND ${CMAKE_COMMAND} --build "@CMAKE_CURRENT_BINARY_DIR@" --target UpdateVerification)
+  execute_process(COMMAND ${CMAKE_COMMAND} --build "@CMAKE_CURRENT_BINARY_DIR@/data" --target UpdateVerification)
 elseif(TYPE STREQUAL "jar")
-  execute_process(COMMAND ${CMAKE_COMMAND} --build "@CMAKE_CURRENT_BINARY_DIR@" --target PulseJava)
+  execute_process(COMMAND ${CMAKE_COMMAND} --build "@CMAKE_CURRENT_BINARY_DIR@/src/java" --target PulseJava)
 elseif(TYPE STREQUAL "rebase")
   # find Git and if available set GIT_HASH variable
   find_package(Git QUIET)
@@ -119,8 +119,25 @@ elseif(TYPE STREQUAL "FullReport")
   execute_process(COMMAND "${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}" com.kitware.pulse.utilities.csv.plots.CSVPlotTool ${ARG1})
+elseif(${TYPE} MATCHES "compare")
+  # If ARG2 is empty, assume ARG1 is a directory with 2 csv files
+  if(NOT ARG2)
+    file(GLOB _csv_files "${ARG1}/*.csv")
+    list(LENGTH _csv_files _num_csv_files)
+    if(_num_csv_files EQUAL 2)
+      list(GET _csv_files 0 _csv_0)
+      list(GET _csv_files 1 _csv_1)
+      message(STATUS "CSV 0 : ${_csv_0}")
+      message(STATUS "CSV 1 : ${_csv_1}")
+      execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.utilities.csv.plots.CSVComparePlotter ${_csv_0} ${_csv_1})
+    else()
+      message(FATAL_ERROR "Could not find 2 csv files in provided directory ${ARG1}")
+    endif()
+  else()
+    execute_process(COMMAND "${Java_JAVA_EXECUTABLE}" -classpath "${JAVA_CLASSPATH}" com.kitware.pulse.utilities.csv.plots.CSVComparePlotter ${ARG1} ${ARG2})
+  endif()
 else()
-  if(${TYPE} MATCHES "Plot")
+  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)

bin/run.sh

 # Refer to the Running and Testing Section in the ReadMe.md for %1 options
 
-cmake -DTYPE:STRING=$1 -P run.cmake
+cmake -DTYPE:STRING=$1 -DARG1:STRING=$2 -DARG2:STRING=$3 -P run.cmake

cmake/PulseConfigBuild.cmake.in

+@PACKAGE_INIT@
+
+set(export_config_name "@export_config_name@")
+
+set_and_check(${export_config_name}Targets "${CMAKE_CURRENT_LIST_DIR}/${export_config_name}Targets.cmake")
+
+include(${${export_config_name}Targets})
+
+
+set(Pulse_ROOT ${PACKAGE_PREFIX_DIR})
+
+if(@Pulse_USING_PROTOBUF_DIR@)
+  set(protobuf_DIR "@protobuf_DIR@")
+  find_package(protobuf REQUIRED CONFIG NO_DEFAULT_PATH)
+else()
+  find_package(protobuf QUIET CONFIG NO_DEFAULT_PATH)
+  if(NOT protobuf_FOUND)
+    find_package(Protobuf REQUIRED)
+  endif()
+endif()

cmake/PulseConfig.cmake.in → cmake/PulseConfigInstall.cmake.in

@@ -10,8 +10,8 @@ include(${${export_config_name}Targets})
 set(Pulse_ROOT ${PACKAGE_PREFIX_DIR})
 
 # Pulse uses protobuf, but only distributes/needs its libraries
-if (NOT protobuf::libprotobuf_FOUND)
- add_library(protobuf::libprotobuf INTERFACE IMPORTED)
- target_link_libraries(protobuf::libprotobuf INTERFACE debug ${PACKAGE_PREFIX_DIR}/lib/@PROTOBUF_LIBRARY_DEBUG@)
- target_link_libraries(protobuf::libprotobuf INTERFACE optimized ${PACKAGE_PREFIX_DIR}/lib/@PROTOBUF_LIBRARY_RELEASE@)
+if (NOT TARGET protobuf::libprotobuf)
+  add_library(protobuf::libprotobuf INTERFACE IMPORTED)
+  target_link_libraries(protobuf::libprotobuf INTERFACE debug ${PACKAGE_PREFIX_DIR}/lib/@PROTOBUF_LIBRARY_DEBUG@)
+  target_link_libraries(protobuf::libprotobuf INTERFACE optimized ${PACKAGE_PREFIX_DIR}/lib/@PROTOBUF_LIBRARY_RELEASE@)
 endif()

cmake/external/CMakeLists.txt

@@ -121,7 +121,8 @@ if (${PROJECT_NAME}_JAVA_API)
   add_dependencies(PulseData Pulse)
   add_custom_command(TARGET PulseData POST_BUILD
       COMMAND ${CMAKE_COMMAND} -DTYPE:STRING=genData -P run.cmake
-              WORKING_DIRECTORY ${CMAKE_INSTALL_PREFIX}/bin)
+              WORKING_DIRECTORY ${CMAKE_INSTALL_PREFIX}/bin
+      BYPRODUCTS "${CMAKE_INSTALL_PREFIX}/bin/patients/StandardMale.json")
   # Don't genStates if in Debug, takes way too long
   string(APPEND _genStates
     "$<IF:$<CONFIG:Debug>,"
@@ -131,7 +132,8 @@ if (${PROJECT_NAME}_JAVA_API)
   add_custom_command(TARGET PulseData POST_BUILD
       COMMAND "${_genStates}"
               COMMAND_EXPAND_LISTS
-              WORKING_DIRECTORY ${CMAKE_INSTALL_PREFIX}/bin)
+              WORKING_DIRECTORY ${CMAKE_INSTALL_PREFIX}/bin
+      BYPRODUCTS "${CMAKE_INSTALL_PREFIX}/bin/states/StandardMale@0s.json")
   set_target_properties (PulseData PROPERTIES FOLDER ${PROJECT_NAME})
 else()
   message(STATUS "!!! Without Java Utils, this build will not generate required data files needed for Pulse to execute !!!")

cmake/external/External_Dirent.cmake

@@ -4,10 +4,10 @@
 include(AddExternalProject)
 define_external_dirs_ex( Dirent )
 add_external_project_ex( Dirent
-  URL "https://github.com/tronkko/dirent/archive/1.22.zip"
-  URL_HASH MD5=cf5b4499d163604732f4dc91654056be
+  URL "https://github.com/tronkko/dirent/archive/1.23.2.zip"
+  URL_HASH MD5=43514791ab73ef5ac7c490afc7c3bab2
   CMAKE_CACHE_ARGS
-      -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX}
+    -DDIRENT_BUILD_TESTS:BOOL=OFF
   RELATIVE_INCLUDE_PATH ""
   DEPENDENCIES ""
   #VERBOSE

cmake/external/External_Eigen3.cmake

@@ -7,8 +7,7 @@ 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
   CMAKE_CACHE_ARGS 
-        -DCMAKE_INSTALL_PREFIX:PATH=${Eigen3_PREFIX}/install
-        -DBUILD_TESTING:BOOL=OFF
+    -DBUILD_TESTING:BOOL=OFF
   RELATIVE_INCLUDE_PATH ""
   DEPENDENCIES ""
   #VERBOSE

cmake/external/External_protobuf.cmake

@@ -38,5 +38,5 @@ if (NOT USE_SYSTEM_protobuf)
     set(protobuf_DIR ${protobuf_PREFIX}/install/lib/cmake/protobuf)
   endif()
   message(STATUS "protobuf_DIR : ${protobuf_DIR}")
+  set(protobuf_SRC ${protobuf_PREFIX}/src)
 endif()
-set(protobuf_SRC ${protobuf_PREFIX}/src)

data/CMakeLists.txt

 # External Data
 include(ExternalData)
-set(ExternalData_URL_TEMPLATES "https://data.kitware.com/api/v1/file/hashsum/%(algo)/%(hash)/download")
+# Putting in the same URL to ensure bad connections retry a few times
+set(ExternalData_URL_TEMPLATES "https://data.kitware.com/api/v1/file/hashsum/%(algo)/%(hash)/download"
+                               "https://data.kitware.com/api/v1/file/hashsum/%(algo)/%(hash)/download"
+                               "https://data.kitware.com/api/v1/file/hashsum/%(algo)/%(hash)/download")
 
 message(STATUS "Looking for zip shas")
 file(GLOB_RECURSE _VERIFICATION_SHA RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} "*.sha512")
@@ -22,7 +25,7 @@ endforeach()
 ExternalData_Add_Target(ExternalData)
 set(ExternalData_LINK_CONTENT SHA512)
 set(ExternalData_TIMEOUT_ABSOLUTE 300)
-set(ExternalData_TIMEOUT_INACTIVITY 60)
+set(ExternalData_TIMEOUT_INACTIVITY 150)
 
 set(INC_DOWNLOAD)
 if(PULSE_DOWNLOAD_BASELINES)

data/config/CDMUnitTests.config

@@ -136,14 +136,17 @@ FluidCircuit = CDMUnitTest
 ThermalCircuit = CDMUnitTest
 ElectricalCircuit = CDMUnitTest
 CombinedCircuit = CDMUnitTest
-InterCircuitComparison = CDMUnitTest
-InterCircuitIndividual = CDMUnitTest Results=InterCircuitIndividual1,InterCircuitIndividual2
 DynamicallyChangingCircuit = CDMUnitTest
 NonZeroReferenceNegative = CDMUnitTest
 NonZeroReferencePositive = CDMUnitTest
 PolarizedCapacitor = CDMUnitTest
 PreChargeComplianceZeroVolume = CDMUnitTest
 PreChargeComplianceNonZeroVolume = CDMUnitTest
+#BasicBlackBoxComparisonTest = CDMUnitTest
+#BasicBlackBoxTest = CDMUnitTest
+#SimpleBlackBoxTest = CDMUnitTest
+#WindkesselBlackBoxTest = CDMUnitTest
+
 #This test is not flushed out, and that's ok
 #CircuitErrorTest = CDMUnitTest
 CircuitLockingTest = CDMUnitTestDriver NoCompare Computed=./test_results/unit_tests/cdm/

data/config/DebugRun.config

@@ -32,4 +32,3 @@ Macro EngineUnitTestFull=EngineUnitTestDriver FullPlot Baseline=unit_tests/pulse
 Macro ScenarioTest=ScenarioTestDriver FastPlot Baseline=scenarios/ Computed=./test_results/scenarios
 
 patient/BasicStandard.json = ScenarioTest
-

data/config/ScenarioVerification.config

@@ -52,6 +52,7 @@ patient/CPRForce.json = ScenarioTest
 patient/DyspneaVaried.json = ScenarioTest
 patient/EffusionCondition.json = ScenarioTest
 patient/EffusionConditionPlus.json = ScenarioTest
+patient/HemorrhageClass1Femoral.json = ScenarioTest
 patient/HemorrhageClass2Blood.json = ScenarioTest
 patient/HemorrhageClass2BrachialArtery.json = ScenarioTest
 patient/HemorrhageClass2InternalMultiple.json = ScenarioTest
@@ -60,13 +61,19 @@ patient/HemorrhageClass2NoFluid.json = ScenarioTest
 patient/HemorrhageClass2Saline.json = ScenarioTest
 patient/HemorrhageClass3NoFluid.json = ScenarioTest
 patient/HemorrhageClass3PackedRBC.json = ScenarioTest
+patient/HemorrhageClass4NoFluid.json = ScenarioTest
 patient/HemorrhageGroup1.json = ScenarioTest
 patient/HemorrhageGroup2.json = ScenarioTest
 patient/HemorrhageGroup3.json = ScenarioTest
 patient/HemorrhageGroup4.json = ScenarioTest
 patient/HemorrhageGroup5.json = ScenarioTest
 patient/HemorrhageGroup6.json = ScenarioTest
+patient/HemorrhageInternalSeverity.json = ScenarioTest
+patient/HemorrhageSeverity1.json = ScenarioTest
+patient/HemorrhageSeverityMultipleCompartments.json = ScenarioTest
+patient/HemorrhageSeverityToFlowToSeverity.json = ScenarioTest
 patient/HemorrhageToShock.json = ScenarioTest
+patient/HemorrhageVaryingSeverity.json = ScenarioTest
 patient/LobarPneumoniaExacerbation.json = ScenarioTest
 patient/LobarPneumoniaModerateBothLungs.json = ScenarioTest
 patient/LobarPneumoniaSevereLeftLobe.json = ScenarioTest

data/human/adult/baselines/scenarios/combined/Cynthia.zip.sha512

-aee907f81221bf66243954c0329c326e0957441b34b9b7a4a7e397041161747306ce2ac8de52b2fee5e6cbb85c88d3fc22f075e4d91d6cbca5221b0066135689
\ No newline at end of file
+a94475d457ebd784e93c80c2537854b05a798bc31359ccbffdfadbbb14f717f80f2043df52735c0c896e00c34cb5dfe833ccfdad65f3dd5ab43d312589c7125f
\ No newline at end of file

data/human/adult/baselines/scenarios/combined/Gus.zip.sha512

-dfd6c4f17d68a238a97eef9c046c77e6431023d04d03bce0246c1e2eea882e2ebf73ab0e46cd2e1f31c7b34a7c80014ed3466541bfa78d559c6306706c1cdd76
\ No newline at end of file
+aa5c58d9e461d48ac53f26ec010fc0e54cc2938215e97c305d85c1be5c61f26172d0d07a3c513185379317fc4ea0b939094b737f31bb51326e0b16269e36db4d
\ No newline at end of file

data/human/adult/baselines/scenarios/combined/Hassan.zip.sha512

-ddaa3c3e98f6aba700d31bdbc314f63db1c72c4f5f576ef5a0ee3803ad9e580969af846619eb5f72f8868c5333fc922b2d763cca1746cdfcbff0c6cbd5d4f0d2
\ No newline at end of file
+1f03a5e697c054474caa454cf5f94baba5d5df431885ac08415ab3ba10dd2c630ae1db73c2d2621fc4082380cce672b0d4731cd04eea019f25fce86b4a30b1b9
\ No newline at end of file

data/human/adult/baselines/scenarios/combined/Joel.zip.sha512

-4e3825860e1add6bee1fe0aaf1c21ae7483b67ceb403ba3fe2815623bd92736ea5592cf412e19e553fae1ea008c37107cc307dc78d69ef584de0b2250fab2459
\ No newline at end of file
+17e6c49a7640b21a795f3a23e291e4ef68abf462bcffd355db10909a194ef60e7b71534571a017dc8a1f0b6a55e9ab3010f8c898a109e8a3b66e38e83ff37aa1
\ No newline at end of file

data/human/adult/baselines/scenarios/combined/Nathan.zip.sha512

-5aaa92c67d1090bc37f29e2be027e9dfcbe22b5a0bd2152d0dfe7f990cd35c23eb8733bcb194a47f4105479a1330084fa89f40a3b988d7a65d8261b1c0a5c4bc
\ No newline at end of file
+59baa74120c2e40bc84cdc043e0370d8bc1c07bfaff8b5a91c43aa944e485b908069dec708f3a09bd27bff85443cb8411d0ef288cbdc958f4e058d77628f4717
\ No newline at end of file

data/human/adult/baselines/scenarios/compartments/AnesthesiaMachineCompartments.zip.sha512

-ab52d83d0b0833184cda7d5dd50bb6019e4acf59fb1431e6dd68b281dca16c32c04a0b455c79f9d60988deaf055f6f100eb89b71ff38ac5218c31176b78f8d61
\ No newline at end of file
+977722162892f4463667b38178b99a854db4c790e92b97b7bfb0a3e2f1ae35d76cf74b9373de6fbdc77d9295774edf111e348494e3315c3ba9df5647a5c05d53
\ No newline at end of file