diff --git a/deploy/alpha_6.2_58_vcellservice.include b/deploy/alpha_6.2_58_vcellservice.include index 913897942b..36245e37a3 100755 --- a/deploy/alpha_6.2_58_vcellservice.include +++ b/deploy/alpha_6.2_58_vcellservice.include @@ -95,7 +95,7 @@ vcell_I4J_pathto_secretsDir=/usr/local/deploy vcell_I4J_use_vagrant=false vcell_I4J_install_jres_into_user_home=false vcell_I4J_updateSiteBaseUrl=http://vcell.org/webstart/$vcell_site_camel -vcell_I4J_pathto_mavenRootDir=/opt/build/VCell +vcell_I4J_pathto_mavenRootDir=/opt/build/vcell vcell_I4J_pathto_installerFile=${vcell_I4J_pathto_mavenRootDir}/deploy/client/install4j/VCell.install4j vcell_I4J_pathto_vcellIcnsFile=${vcell_I4J_pathto_mavenRootDir}/deploy/client/install4j/icons/vcell.icns vcell_I4J_pathto_jreDir=$HOME/.install4j6/jres diff --git a/deploy/alpha_6.2_59_vcellservice.include b/deploy/alpha_6.2_59_vcellservice.include new file mode 100755 index 0000000000..60acd511ac --- /dev/null +++ b/deploy/alpha_6.2_59_vcellservice.include @@ -0,0 +1,118 @@ +#!/usr/bin/env bash + +shopt -s -o nounset + +_site="alpha" +_version="6.2" +_build="59" +vcell_server_os="linux64" + +vcell_site_lower=`echo $_site | tr '[:upper:]' '[:lower:]'` +vcell_site_upper=`echo $_site | tr '[:lower:]' '[:upper:]'` +vcell_site_camel="${vcell_site_upper:0:1}${vcell_site_lower:1:100}" +vcell_version=${_version} +vcell_build=${_build} +vcell_softwareVersionString="${vcell_site_camel}_Version_${vcell_version}_build_${vcell_build}" +unset _site +unset _version +unset _build + +vcell_applicationId="1471-8022-1038-5554" +vcell_server_sitedir="/share/apps/vcell2/deployed_new/$vcell_site_lower" +vcell_pathto_sitedir="/share/apps/vcell2/deployed_new/$vcell_site_lower" + +vcell_user="vcell" +vcell_servicehost="vcell-service.cam.uchc.edu" +vcell_apihost="vcellapi.cam.uchc.edu" +vcell_apiport=8080 + +# +# Nagios monitor port +# (rel=33330, beta=33331, alpha=33332, test=-33333, test2=-33334, test3=-33335, test4=-33336) +# +vcell_monitor_queryport=33332 + +vcell_rmihost="vcell-rmi-alpha.cam.uchc.edu" +vcell_rmiport_low=-1 +vcell_rmiport_high=40106 +vcell_rmihosts="vcell-rmi-alpha.cam.uchc.edu:40106" +# still using bioformats_ALPHA_6_2_54.jar for later versions ... need to replace with ImageJ support. +vcell_bioformatsJarFile="bioformats_ALPHA_6_2_54.jar" +vcell_bioformatsJarDownloadURL="http://vcell.org/webstart/$vcell_site_camel/$vcell_bioformatsJarFile" + +vcell_vcellClientJarFileName="vcell-client-0.0.1-SNAPSHOT.jar" +vcell_vcellServerJarFileName="vcell-server-0.0.1-SNAPSHOT.jar" +vcell_vcellApiJarFileName="vcell-api-0.0.1-SNAPSHOT.jar" +vcell_vcellAdminJarFileName="vcell-admin-0.0.1-SNAPSHOT.jar" + +vcell_jms_url="failover:(tcp://code2.cam.uchc.edu:61617)?timeout=120000" +vcell_jms_user=clientUser + +# +# Oracle on server +# +vcell_database_url="jdbc:oracle:thin:@VCELL-DB.cam.uchc.edu:1521/vcelldborcl.cam.uchc.edu" +vcell_database_driver=oracle.jdbc.driver.OracleDriver +vcell_database_user=vcell + +# +# Postgres on locahost +# +#vcell_database_url="jdbc:postgresql://localhost:5432/schaff" +#vcell_database_driver=org.postgresql.Driver +#vcell_database_user=schaff + +vcell_amplistor_url="http://obj1.cam.uchc.edu:8080/namespace/service_vcell/" +vcell_amplistor_user=vcell + +vcell_mongodb_host=mongo.cam.uchc.edu +vcell_mongodb_port=27017 +vcell_mongodb_database=$vcell_site_upper +vcell_mongodb_collection=logging + +vcell_smtp_host=vdsmtp.cam.uchc.edu +vcell_smtp_port=25 +vcell_smtp_email="VCell_Support@uchc.edu" + +vcell_common_jre=/share/apps/vcell2/java/jdk1.8.0_66/bin/java +vcell_common_jre_rmi=/usr/java/jdk1.8.0_66/jre/bin/java + +vcell_rmiservice_high_jmxport=12305 +vcell_rmiservice_http_jmxport=12304 +vcell_vcellservice_jmxport=12360 + +vcell_primary_datadir=/share/apps/vcell3/users/ +vcell_secondary_datadir=/share/apps/vcell3/users/ +vcell_parallel_datadir=/state/partition1/vcelltemp/ +vcell_export_dir=/share/apps/vcell2/export/ +vcell_export_url=http://vcell.org/export/ + +vcell_mpich_homedir="/share/apps/vcell2/mpich/" + +vcell_secretsDir=/usr/local/deploy +vcell_I4J_pathto_secretsDir=/usr/local/deploy + +vcell_I4J_use_vagrant=false +vcell_I4J_install_jres_into_user_home=false +vcell_I4J_updateSiteBaseUrl=http://vcell.org/webstart/$vcell_site_camel +vcell_I4J_pathto_mavenRootDir=/opt/build/vcell +vcell_I4J_pathto_installerFile=${vcell_I4J_pathto_mavenRootDir}/deploy/client/install4j/VCell.install4j +vcell_I4J_pathto_vcellIcnsFile=${vcell_I4J_pathto_mavenRootDir}/deploy/client/install4j/icons/vcell.icns +vcell_I4J_pathto_jreDir=$HOME/.install4j6/jres +vcell_I4J_jreDir=$HOME/.install4j6/jres +vcell_I4J_pathto_install4jc=/opt/install4j6/bin/install4jc + +vcell_htc_usessh=false +# +#if [ "$vcell_htc_usessh" = true ]; then +# # +# # only define these if using ssh to invoke the htc processes +# # +# # DSA Keystore is for password-less authentication to HTC host +# # +# vcell_htc_sshhost="vcell-service.cam.uchc.edu" +# vcell_htc_sshuser="vcell" +# vcell_htc_sshDsaKeyFile="/Users/schaff/.ssh/schaff_dsa" +#fi +# + diff --git a/deploy/deploy.sh b/deploy/deploy.sh old mode 100644 new mode 100755 index ec22711151..016e75d903 --- a/deploy/deploy.sh +++ b/deploy/deploy.sh @@ -13,8 +13,10 @@ includefile=$1 . $vcell_secretsDir/deploySecrets.include DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" +echo "deploy directory is ${DIR}" projectRootDir=`dirname $DIR` +echo "project root directory is ${projectRootDir}" projectTargetDir=$projectRootDir/target serverTargetDir=$projectRootDir/vcell-server/target @@ -31,6 +33,12 @@ clientJarsDir=$clientTargetDir/maven-jars skip_install4j=false skip_build=false +skip_download_solvers=false + +if [ "$skip_download_solvers" = false ]; then + installSolversScript="${projectRootDir}/localsolvers/installSolvers.sh" + $installSolversScript +fi #-------------------------------------------------------------------------- # build project, generate user help files, gather jar files @@ -564,4 +572,4 @@ else echo "" echo " then, don't forget to update symbolic links to installers" echo "" -fi \ No newline at end of file +fi diff --git a/localsolvers/README.md b/localsolvers/README.md new file mode 100644 index 0000000000..c70dfa70b8 --- /dev/null +++ b/localsolvers/README.md @@ -0,0 +1,11 @@ +Solvers are no longer included as binary artifacts within this source distribution + +please see the vcell-solvers project on github for binaries associated with releases. + +The solver archives associated with each platform are available as follows: + +linux32.tgz - not yet available from github. +linux64.tgz - https://github.com/virtualcell/vcell-solvers/releases/download/binaries_20170901/linux64.tgz +macos.tgz - https://github.com/virtualcell/vcell-solvers/releases/download/binaries_20170901/macos.tgz +win32.tgz - not yet available from github. +win64.tgz - https://github.com/virtualcell/vcell-solvers/releases/download/binaries_20170901/win64.tgz diff --git a/localsolvers/installSolvers.cmd b/localsolvers/installSolvers.cmd new file mode 100644 index 0000000000..c1a890c1eb --- /dev/null +++ b/localsolvers/installSolvers.cmd @@ -0,0 +1,30 @@ + +@echo "1) download the following urls (one for each platform) +@echo "2) extract the archive using 7-zip or similar archive utility +@echo "3) place extracted solver binaries into corresponding subdirectory of localsolvers" + +@echo " (for 64-bit Windows)" +@echo "---win64 url---" +@type win64/url.txt +@echo "---end---" + +@echo " (for MacOS)" +@echo "---mac64 url---" +@type mac64/url.txt +@echo "---end---" + +@echo " (for 64-bit Linux)" +@echo "---linux64 url---" +@type linux64/url.txt +@echo "---end---" + +@echo " (for 32-bit Linux)" +@echo "---linux32 url---" +@type linux32/url.txt +@echo "---end---" + +@echo " (for 32-bit Windows)" +@echo "---win32 url---" +@type win32/url.txt +@echo "---end---" + diff --git a/localsolvers/installSolvers.sh b/localsolvers/installSolvers.sh new file mode 100755 index 0000000000..c41e242cf2 --- /dev/null +++ b/localsolvers/installSolvers.sh @@ -0,0 +1,82 @@ +#!/usr/bin/env bash + +DIR=${0%/*} + +cd $DIR +# +# get win64 solver binaries from url stored in win64/url.txt (assumes single archive that is packaged as tar.gz) +# +if [ -s "${DIR}/win64/url.txt" ]; then + win64_url=$(head -n 1 "${DIR}/win64/url.txt") + echo "curl -L -o win64.tgz $win64_url" + curl -L -o win64.tgz $win64_url + if [ $? -eq 0 ]; then + pushd win64 + tar xzvf ../win64.tgz + popd + rm win64.tgz + fi +fi + +# +# get win32 solver binaries from url stored in win32/url.txt (assumes single archive that is packaged as tar.gz) +# +if [ -s "${DIR}/win32/url.txt" ]; then + win32_url=$(head -n 1 "${DIR}/win32/url.txt") + echo "curl -L -o win32.tgz $win32_url" + curl -L -o win32.tgz $win32_url + if [ $? -eq 0 ]; then + pushd win32 + tar xzvf ../win32.tgz + popd + rm win32.tgz + fi +fi + +# +# get macos (64-bit) solver binaries from url stored in mac64/url.txt (assumes single archive that is packaged as tar.gz) +# +if [ -s "${DIR}/mac64/url.txt" ]; then + mac64_url=$(head -n 1 "${DIR}/mac64/url.txt") + echo "curl -L -o mac64.tgz $mac64_url" + curl -L -o mac64.tgz $mac64_url + if [ $? -eq 0 ]; then + pushd mac64 + tar xzvf ../mac64.tgz + popd + rm mac64.tgz + fi +fi + +# +# get linux64 solver binaries from url stored in linux64/url.txt (assumes single archive that is packaged as tar.gz) +# note that these solvers are the full server-side binaries with the ActiveMQ libraries linked for messaging. +# +if [ -s "${DIR}/linux64/url.txt" ]; then + linux64_url=$(head -n 1 "${DIR}/linux64/url.txt") + echo "curl -L -o linux64.tgz $linux64_url" + curl -L -o linux64.tgz $linux64_url + if [ $? -eq 0 ]; then + pushd linux64 + tar xzvf ../linux64.tgz + popd + rm linux64.tgz + fi +fi + +# +# get linux32 solver binaries from url stored in linux32/url.txt (assumes single archive that is packaged as tar.gz) +# +if [ -s "${DIR}/linux32/url.txt" ]; then + linux32_url=$(head -n 1 "${DIR}/linux32/url.txt") + echo "curl -L -o linux32.tgz $linux32_url" + curl -L -o linux32.tgz $linux32_url + if [ $? -eq 0 ]; then + pushd linux32 + tar xzvf ../linux32.tgz + popd + rm linux32.tgz + fi +fi + + diff --git a/localsolvers/linux32/FiniteVolume b/localsolvers/linux32/FiniteVolume deleted file mode 100755 index 857c908ff0..0000000000 Binary files a/localsolvers/linux32/FiniteVolume and /dev/null differ diff --git a/localsolvers/linux32/Hybrid_EM b/localsolvers/linux32/Hybrid_EM deleted file mode 100755 index c0f92a6190..0000000000 Binary files a/localsolvers/linux32/Hybrid_EM and /dev/null differ diff --git a/localsolvers/linux32/Hybrid_MIL b/localsolvers/linux32/Hybrid_MIL deleted file mode 100755 index 6ae419b63b..0000000000 Binary files a/localsolvers/linux32/Hybrid_MIL and /dev/null differ diff --git a/localsolvers/linux32/Hybrid_MIL_Adaptive b/localsolvers/linux32/Hybrid_MIL_Adaptive deleted file mode 100755 index dae06f00d3..0000000000 Binary files a/localsolvers/linux32/Hybrid_MIL_Adaptive and /dev/null 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cdaa1bbbf7..0000000000 Binary files a/localsolvers/mac64/smoldyn_x64 and /dev/null differ diff --git a/localsolvers/mac64/url.txt b/localsolvers/mac64/url.txt new file mode 100644 index 0000000000..e4140d8238 --- /dev/null +++ b/localsolvers/mac64/url.txt @@ -0,0 +1 @@ +https://github.com/virtualcell/vcell-solvers/releases/download/binaries_20170901/macos.tgz diff --git a/localsolvers/win32/README.txt b/localsolvers/win32/README.txt deleted file mode 100644 index 45e61a1214..0000000000 --- a/localsolvers/win32/README.txt +++ /dev/null @@ -1 +0,0 @@ -32 bit windows solvers \ No newline at end of file diff --git a/localsolvers/win32/url.txt b/localsolvers/win32/url.txt new file mode 100644 index 0000000000..8b13789179 --- /dev/null +++ b/localsolvers/win32/url.txt @@ -0,0 +1 @@ + diff --git a/localsolvers/win64/FiniteVolume_x64.exe b/localsolvers/win64/FiniteVolume_x64.exe deleted file mode 100644 index 4b1751e95c..0000000000 Binary files a/localsolvers/win64/FiniteVolume_x64.exe and /dev/null differ diff --git a/localsolvers/win64/MovingBoundary_x64.exe b/localsolvers/win64/MovingBoundary_x64.exe deleted file mode 100644 index 6f3b17ed81..0000000000 Binary files a/localsolvers/win64/MovingBoundary_x64.exe and /dev/null differ diff --git a/localsolvers/win64/NFsim_x64.exe b/localsolvers/win64/NFsim_x64.exe deleted file mode 100644 index 30dbfac683..0000000000 Binary files a/localsolvers/win64/NFsim_x64.exe and /dev/null differ diff --git a/localsolvers/win64/SundialsSolverStandalone_x64.exe b/localsolvers/win64/SundialsSolverStandalone_x64.exe deleted file mode 100644 index abbfa769f6..0000000000 Binary files a/localsolvers/win64/SundialsSolverStandalone_x64.exe and /dev/null differ diff --git a/localsolvers/win64/VCellStoch_x64.exe b/localsolvers/win64/VCellStoch_x64.exe deleted file mode 100644 index a9c6f8ee5e..0000000000 Binary files a/localsolvers/win64/VCellStoch_x64.exe and /dev/null differ diff --git a/localsolvers/win64/libgcc_s_seh-1.dll b/localsolvers/win64/libgcc_s_seh-1.dll deleted file mode 100644 index c2cb099075..0000000000 Binary files a/localsolvers/win64/libgcc_s_seh-1.dll and /dev/null differ diff --git a/localsolvers/win64/libgfortran-3.dll b/localsolvers/win64/libgfortran-3.dll deleted file mode 100644 index fb3554553a..0000000000 Binary files a/localsolvers/win64/libgfortran-3.dll and /dev/null differ diff --git a/localsolvers/win64/libhdf5-0.dll b/localsolvers/win64/libhdf5-0.dll deleted file mode 100644 index 671d077a58..0000000000 Binary files a/localsolvers/win64/libhdf5-0.dll and /dev/null differ diff --git a/localsolvers/win64/libhdf5_cpp-0.dll b/localsolvers/win64/libhdf5_cpp-0.dll deleted file mode 100644 index 2f6ebbb5a8..0000000000 Binary files a/localsolvers/win64/libhdf5_cpp-0.dll and /dev/null differ diff --git a/localsolvers/win64/libquadmath-0.dll b/localsolvers/win64/libquadmath-0.dll deleted file mode 100644 index 60ec3aa68f..0000000000 Binary files a/localsolvers/win64/libquadmath-0.dll and /dev/null differ diff --git a/localsolvers/win64/libstdc++-6.dll b/localsolvers/win64/libstdc++-6.dll deleted file mode 100644 index d53101e7ee..0000000000 Binary files a/localsolvers/win64/libstdc++-6.dll and /dev/null differ diff --git a/localsolvers/win64/libszip-0.dll b/localsolvers/win64/libszip-0.dll deleted file mode 100644 index 7ec3223404..0000000000 Binary files a/localsolvers/win64/libszip-0.dll and /dev/null differ diff --git a/localsolvers/win64/libwinpthread-1.dll b/localsolvers/win64/libwinpthread-1.dll deleted file mode 100644 index 11a98619aa..0000000000 Binary files a/localsolvers/win64/libwinpthread-1.dll and /dev/null differ diff --git a/localsolvers/win64/libzip-5.dll b/localsolvers/win64/libzip-5.dll deleted file mode 100644 index 12e6bf47fd..0000000000 Binary files a/localsolvers/win64/libzip-5.dll and /dev/null differ diff --git a/localsolvers/win64/prop.txt b/localsolvers/win64/prop.txt deleted file mode 100644 index e69de29bb2..0000000000 diff --git a/localsolvers/win64/smoldyn_x64.exe b/localsolvers/win64/smoldyn_x64.exe deleted file mode 100644 index 3f8b074e9e..0000000000 Binary files a/localsolvers/win64/smoldyn_x64.exe and /dev/null differ diff --git a/localsolvers/win64/url.txt b/localsolvers/win64/url.txt new file mode 100644 index 0000000000..8856a8690b --- /dev/null +++ b/localsolvers/win64/url.txt @@ -0,0 +1 @@ +https://github.com/virtualcell/vcell-solvers/releases/download/binaries_20170901/win64.tgz diff --git a/localsolvers/win64/zlib1.dll b/localsolvers/win64/zlib1.dll deleted file mode 100644 index 1f16088805..0000000000 Binary files a/localsolvers/win64/zlib1.dll and /dev/null differ diff --git a/vcell-client/jsbml.log b/vcell-client/jsbml.log index ccfafbfbeb..e0ec0ece0d 100644 --- a/vcell-client/jsbml.log +++ b/vcell-client/jsbml.log @@ -1,3 +1,242 @@ 2017-08-12 02:55:35,138 WARN c.v.r.PropertyLoader [main] Can't read propertyFile /Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/vcell.properties specified by java home directory 2017-08-12 02:55:35,147 WARN c.v.u.NativeLoader [main] DYLD_FALLBACK_LIBRARY_PATH not set 2017-08-12 02:55:37,886 ERROR o.v.c.l.LWNamespace [AWT-EventQueue-0] top level object DocumentWindow does not implement ChildWindowManager$ManagedChild +2017-08-30 21:06:36,812 WARN c.v.r.PropertyLoader [main] Can't read propertyFile /Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/vcell.properties specified by java home directory +2017-08-30 21:06:36,827 WARN c.v.u.NativeLoader [main] DYLD_FALLBACK_LIBRARY_PATH not set +2017-08-30 21:06:58,091 ERROR o.v.c.l.LWNamespace [AWT-EventQueue-0] top level object DocumentWindow does not implement ChildWindowManager$ManagedChild +2017-08-31 20:38:16,393 WARN c.v.r.PropertyLoader [main] Can't read propertyFile /Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home/jre/vcell.properties specified by java home directory +2017-08-31 20:38:16,403 WARN c.v.u.NativeLoader [main] DYLD_FALLBACK_LIBRARY_PATH not set +2017-08-31 20:38:25,666 ERROR o.v.c.l.LWNamespace [AWT-EventQueue-0] top level object DocumentWindow does not implement ChildWindowManager$ManagedChild +2017-08-31 20:38:55,149 WARN o.v.c.l.LWDialog [AWT-EventQueue-0] IndefiniteProgressDialog WORKING... invalid modeless dialog +2017-08-31 20:38:55,149 WARN o.v.c.l.LWDialog [AWT-EventQueue-0] IndefiniteProgressDialog WORKING... invalid modeless dialog +2017-08-31 20:38:55,688 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element adjacentDomains is not part of the SBML specifications (AdjacentDomains). +2017-08-31 20:38:55,692 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element adjacentDomains is not part of the SBML specifications (AdjacentDomains). +2017-08-31 20:38:55,693 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element adjacentDomains is not part of the SBML specifications (AdjacentDomains). +2017-08-31 20:38:55,693 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element adjacentDomains is not part of the SBML specifications (AdjacentDomains). +2017-08-31 20:38:55,697 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element boundaryMin is not part of the SBML specifications (Boundary). +2017-08-31 20:38:55,698 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element boundaryMax is not part of the SBML specifications (Boundary). +2017-08-31 20:38:55,698 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element boundaryMin is not part of the SBML specifications (Boundary). +2017-08-31 20:38:55,699 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element boundaryMax is not part of the SBML specifications (Boundary). +2017-08-31 20:38:55,700 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element boundaryMin is not part of the SBML specifications (Boundary). +2017-08-31 20:38:55,700 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element boundaryMax is not part of the SBML specifications (Boundary). +2017-08-31 20:38:55,701 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element domain is not part of the SBML specifications (Domain). +2017-08-31 20:38:55,703 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element domain is not part of the SBML specifications (Domain). +2017-08-31 20:38:55,704 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element domain is not part of the SBML specifications (Domain). +2017-08-31 20:38:55,705 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element domain is not part of the SBML specifications (Domain). +2017-08-31 20:38:55,705 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element domain is not part of the SBML specifications (Domain). +2017-08-31 20:38:55,708 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element sampledFieldGeometry is not part of the SBML specifications (SampledFieldGeometry). +2017-08-31 20:38:55,709 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element sampledVolume is not part of the SBML specifications (SampledVolume). +2017-08-31 20:38:55,710 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element sampledVolume is not part of the SBML specifications (SampledVolume). +2017-08-31 20:38:55,710 WARN o.s.j.x.p.AbstractReaderWriter [ClientTaskDispatcher 2 Importing document] processAttribute: The attribute 'id' on the element sampledVolume is not part of the SBML specifications (SampledVolume). +2017-08-31 20:38:57,722 INFO c.v.g.s.GeometrySurfaceUtils [ClientTaskDispatcher 2 Importing document] RegionInfo(regionIndex=0, numPixel=1951497, imageValue=0) +2017-08-31 20:38:57,735 INFO c.v.g.s.GeometrySurfaceUtils [ClientTaskDispatcher 2 Importing document] size=124825.89972223382 +2017-08-31 20:38:57,736 INFO c.v.g.s.GeometrySurfaceUtils [ClientTaskDispatcher 2 Importing document] added volumeRegion(domainType_ec0) +2017-08-31 20:38:57,736 INFO c.v.g.s.GeometrySurfaceUtils [ClientTaskDispatcher 2 Importing document] RegionInfo(regionIndex=1, numPixel=221707, imageValue=1) +2017-08-31 20:38:57,745 INFO c.v.g.s.GeometrySurfaceUtils [ClientTaskDispatcher 2 Importing document] size=14800.809866464228 +2017-08-31 20:38:57,745 INFO c.v.g.s.GeometrySurfaceUtils [ClientTaskDispatcher 2 Importing document] added volumeRegion(domainType_cytosol1) +2017-08-31 20:38:57,746 INFO c.v.g.s.GeometrySurfaceUtils [ClientTaskDispatcher 2 Importing document] RegionInfo(regionIndex=2, numPixel=55019, imageValue=2) +2017-08-31 20:38:57,752 INFO c.v.g.s.GeometrySurfaceUtils [ClientTaskDispatcher 2 Importing document] size=3674.241229985856 +2017-08-31 20:38:57,753 INFO c.v.g.s.GeometrySurfaceUtils [ClientTaskDispatcher 2 Importing document] added volumeRegion(domainType_Nucleus2) +2017-08-31 20:38:57,753 INFO c.v.g.s.GeometrySurfaceUtils [ClientTaskDispatcher 2 Importing document] RegionInfo(regionIndex=3, numPixel=1, imageValue=1) +2017-08-31 20:38:57,757 INFO c.v.g.s.GeometrySurfaceUtils [ClientTaskDispatcher 2 Importing document] size=0.06678131609054792 +2017-08-31 20:38:57,757 INFO c.v.g.s.GeometrySurfaceUtils [ClientTaskDispatcher 2 Importing document] added volumeRegion(domainType_cytosol3) +2017-08-31 20:38:57,777 INFO c.v.g.s.GeometrySurfaceUtils [ClientTaskDispatcher 2 Importing document] added surfaceRegion(membrane_domainType_ec0_domainType_cytosol1) +2017-08-31 20:38:57,781 INFO c.v.g.s.GeometrySurfaceUtils [ClientTaskDispatcher 2 Importing document] added surfaceRegion(membrane_domainType_cytosol1_domainType_Nucleus2) +2017-08-31 20:38:57,781 INFO c.v.g.s.GeometrySurfaceUtils [ClientTaskDispatcher 2 Importing document] added surfaceRegion(membrane_domainType_ec0_domainType_cytosol3) +2017-08-31 20:38:59,537 WARN c.v.c.d.b.DocumentEditor [AWT-EventQueue-0] can't find window owner +2017-08-31 20:39:16,505 ERROR o.v.c.l.LWNamespace [AWT-EventQueue-0] top level object DocumentWindow does not implement ChildWindowManager$ManagedChild +2017-08-31 20:39:16,507 ERROR o.v.c.l.LWNamespace [AWT-EventQueue-0] top level object DocumentWindow does not implement ChildWindowManager$ManagedChild +2017-08-31 20:39:17,925 WARN o.v.c.l.LWDialog [AWT-EventQueue-0] LinearDefiniteProgressDialog WORKING... invalid modeless dialog +2017-08-31 20:39:17,925 WARN o.v.c.l.LWDialog [AWT-EventQueue-0] LinearDefiniteProgressDialog WORKING... invalid modeless dialog +2017-08-31 20:39:18,303 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] RegionInfo(regionIndex=0, numPixel=110873, imageValue=0) +2017-08-31 20:39:18,304 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] size=124855.88576827208 +2017-08-31 20:39:18,304 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added volumeRegion(domainType_ec0) +2017-08-31 20:39:18,304 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] RegionInfo(regionIndex=1, numPixel=12137, imageValue=1) +2017-08-31 20:39:18,304 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] size=14771.215436625847 +2017-08-31 20:39:18,304 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added volumeRegion(domainType_cytosol1) +2017-08-31 20:39:18,304 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] RegionInfo(regionIndex=2, numPixel=1, imageValue=1) +2017-08-31 20:39:18,305 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] size=1.2185460680272107 +2017-08-31 20:39:18,305 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added volumeRegion(domainType_cytosol2) +2017-08-31 20:39:18,305 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] RegionInfo(regionIndex=3, numPixel=8, imageValue=1) +2017-08-31 20:39:18,305 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] size=9.748368544217685 +2017-08-31 20:39:18,305 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added volumeRegion(domainType_cytosol3) +2017-08-31 20:39:18,305 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] RegionInfo(regionIndex=4, numPixel=3006, imageValue=2) +2017-08-31 20:39:18,305 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] size=3662.9494804897954 +2017-08-31 20:39:18,305 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added volumeRegion(domainType_Nucleus4) +2017-08-31 20:39:18,306 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added surfaceRegion(membrane_domainType_ec0_domainType_cytosol1) +2017-08-31 20:39:18,306 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added surfaceRegion(membrane_domainType_ec0_domainType_cytosol2) +2017-08-31 20:39:18,306 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added surfaceRegion(membrane_domainType_ec0_domainType_cytosol3) +2017-08-31 20:39:18,307 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added surfaceRegion(membrane_domainType_cytosol1_domainType_Nucleus4) +2017-08-31 20:39:27,053 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:39:27,054 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,054 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,055 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,055 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:39:27,307 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:39:27,307 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,308 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,308 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,308 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:39:27,412 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:39:27,412 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,412 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,412 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,412 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:39:27,547 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:39:27,547 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,547 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,547 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,547 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:39:27,668 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:39:27,668 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,668 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,668 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,668 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:39:27,771 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:39:27,771 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,771 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,771 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,771 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:39:27,901 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:39:27,901 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,902 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,902 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:27,902 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:39:28,005 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:39:28,006 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:28,006 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:28,006 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:28,006 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:39:28,110 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:39:28,110 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:28,110 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:28,110 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:28,110 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:39:28,235 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:39:28,235 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:28,235 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:28,235 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:28,236 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 6 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:39:28,942 ERROR o.v.c.l.LWNamespace [AWT-EventQueue-0] top level object DocumentWindow does not implement ChildWindowManager$ManagedChild +2017-08-31 20:39:34,643 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 9 Setting timepoint=0.5] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:39:34,643 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 9 Setting timepoint=0.5] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:34,644 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 9 Setting timepoint=0.5] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:34,644 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 9 Setting timepoint=0.5] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:34,644 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 9 Setting timepoint=0.5] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:39:34,755 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 9 Setting timepoint=0.5] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:39:34,756 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 9 Setting timepoint=0.5] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:34,756 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 9 Setting timepoint=0.5] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:34,756 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 9 Setting timepoint=0.5] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:34,756 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 9 Setting timepoint=0.5] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:39:34,888 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 9 Setting timepoint=0.5] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:39:34,888 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 9 Setting timepoint=0.5] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:34,888 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 9 Setting timepoint=0.5] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:34,889 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 9 Setting timepoint=0.5] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:34,889 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 9 Setting timepoint=0.5] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:39:42,387 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 10 retrieving data] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:39:42,387 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 10 retrieving data] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:42,387 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 10 retrieving data] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:42,387 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 10 retrieving data] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:42,388 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 10 retrieving data] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:39:42,521 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 10 retrieving data] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:39:42,521 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 10 retrieving data] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:42,521 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 10 retrieving data] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:42,521 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 10 retrieving data] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:39:42,521 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 10 retrieving data] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:45:21,989 WARN o.v.c.l.LWDialog [AWT-EventQueue-0] LinearDefiniteProgressDialog WORKING... invalid modeless dialog +2017-08-31 20:45:21,990 WARN o.v.c.l.LWDialog [AWT-EventQueue-0] LinearDefiniteProgressDialog WORKING... invalid modeless dialog +2017-08-31 20:45:22,192 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] RegionInfo(regionIndex=0, numPixel=110873, imageValue=0) +2017-08-31 20:45:22,193 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] size=124855.88576827208 +2017-08-31 20:45:22,193 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added volumeRegion(domainType_ec0) +2017-08-31 20:45:22,193 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] RegionInfo(regionIndex=1, numPixel=12137, imageValue=1) +2017-08-31 20:45:22,194 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] size=14771.215436625847 +2017-08-31 20:45:22,194 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added volumeRegion(domainType_cytosol1) +2017-08-31 20:45:22,194 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] RegionInfo(regionIndex=2, numPixel=1, imageValue=1) +2017-08-31 20:45:22,194 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] size=1.2185460680272107 +2017-08-31 20:45:22,194 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added volumeRegion(domainType_cytosol2) +2017-08-31 20:45:22,194 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] RegionInfo(regionIndex=3, numPixel=8, imageValue=1) +2017-08-31 20:45:22,195 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] size=9.748368544217685 +2017-08-31 20:45:22,195 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added volumeRegion(domainType_cytosol3) +2017-08-31 20:45:22,195 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] RegionInfo(regionIndex=4, numPixel=3006, imageValue=2) +2017-08-31 20:45:22,195 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] size=3662.9494804897954 +2017-08-31 20:45:22,195 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added volumeRegion(domainType_Nucleus4) +2017-08-31 20:45:22,196 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added surfaceRegion(membrane_domainType_ec0_domainType_cytosol1) +2017-08-31 20:45:22,197 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added surfaceRegion(membrane_domainType_ec0_domainType_cytosol2) +2017-08-31 20:45:22,197 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added surfaceRegion(membrane_domainType_ec0_domainType_cytosol3) +2017-08-31 20:45:22,197 INFO c.v.g.s.GeometrySurfaceUtils [Compiled Solver (cbit.vcell.solvers.FVSolverStandalone)] added surfaceRegion(membrane_domainType_cytosol1_domainType_Nucleus4) +2017-08-31 20:45:30,228 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:45:30,228 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,228 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,228 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,228 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:45:30,329 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:45:30,329 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,329 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,329 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,330 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:45:30,429 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:45:30,429 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,429 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,429 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,429 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:45:30,529 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:45:30,529 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,529 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,529 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,529 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:45:30,645 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:45:30,646 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,646 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,646 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,646 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:45:30,761 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:45:30,761 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,761 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,762 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,762 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:45:30,872 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:45:30,873 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,873 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,873 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,873 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:45:30,956 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:45:30,957 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,957 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,957 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:30,957 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:45:31,045 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:45:31,045 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:31,045 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:31,045 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:31,045 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:45:31,160 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:45:31,160 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:31,160 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:31,160 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:31,160 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 12 Retrieving results] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:45:31,709 ERROR o.v.c.l.LWNamespace [AWT-EventQueue-0] top level object DocumentWindow does not implement ChildWindowManager$ManagedChild +2017-08-31 20:45:34,815 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 15 Setting timepoint=0.5] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:45:34,815 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 15 Setting timepoint=0.5] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:34,815 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 15 Setting timepoint=0.5] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:34,815 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 15 Setting timepoint=0.5] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:34,815 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 15 Setting timepoint=0.5] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:45:34,901 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 15 Setting timepoint=0.5] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:45:34,902 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 15 Setting timepoint=0.5] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:34,902 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 15 Setting timepoint=0.5] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:34,902 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 15 Setting timepoint=0.5] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:34,902 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 15 Setting timepoint=0.5] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:45:35,004 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 15 Setting timepoint=0.5] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:45:35,004 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 15 Setting timepoint=0.5] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:35,004 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 15 Setting timepoint=0.5] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:35,005 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 15 Setting timepoint=0.5] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:35,005 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 15 Setting timepoint=0.5] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:45:40,452 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 16 retrieving data] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:45:40,452 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 16 retrieving data] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:40,452 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 16 retrieving data] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:40,453 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 16 retrieving data] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:40,453 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 16 retrieving data] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus +2017-08-31 20:45:40,543 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 16 retrieving data] Token('0', line=11, col=10) comments AFTER: domainType_ec +2017-08-31 20:45:40,543 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 16 retrieving data] Token('1', line=12, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:40,543 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 16 retrieving data] Token('2', line=13, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:40,544 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 16 retrieving data] Token('3', line=14, col=10) comments AFTER: domainType_cytosol +2017-08-31 20:45:40,544 INFO o.v.u.CommentStringTokenizer [ClientTaskDispatcher 16 retrieving data] Token('4', line=15, col=10) comments AFTER: domainType_Nucleus diff --git a/vcell-core/src/main/java/cbit/vcell/microscopy/CurveFitting.java b/vcell-core/src/main/java/cbit/vcell/microscopy/CurveFitting.java index 4a7cb6b965..d4560994be 100644 --- a/vcell-core/src/main/java/cbit/vcell/microscopy/CurveFitting.java +++ b/vcell-core/src/main/java/cbit/vcell/microscopy/CurveFitting.java @@ -33,6 +33,7 @@ import cbit.vcell.opt.Weights; import cbit.vcell.opt.solvers.PowellOptimizationSolver; import cbit.vcell.parser.Expression; +import cbit.vcell.parser.ExpressionBindingException; import cbit.vcell.parser.ExpressionException; import cbit.vcell.parser.SimpleSymbolTable; import cbit.vcell.solver.Simulation; @@ -76,12 +77,7 @@ public static Expression fitBleachWhileMonitoring(double[] time, double[] normal FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getScale(), FRAPModel.REF_BLEACH_WHILE_MONITOR_PARAM.getInitialGuess())}; - ArrayList symbols = new ArrayList(); - symbols.add("t"); - for (Parameter p : parameters){ - symbols.add(p.getName()); - } - modelExp.bindExpression(new SimpleSymbolTable(symbols.toArray(new String[0]))); + bindExpressionToParametersAndTime(modelExp, parameters); // estimate blech while monitoring rate by minimizing the error between funtion values and reference data if(weights == null) @@ -130,6 +126,16 @@ public static Expression fitBleachWhileMonitoring(double[] time, double[] normal return fit; } + private static void bindExpressionToParametersAndTime(Expression modelExp, Parameter[] parameters) + throws ExpressionBindingException { + ArrayList symbols = new ArrayList(); + symbols.add("t"); + for (Parameter p : parameters){ + symbols.add(p.getName()); + } + modelExp.bindExpression(new SimpleSymbolTable(symbols.toArray(new String[0]))); + } + /* * @para: time, time points since the first post bleach. * @para: flour, average intensities under bleached region according to time points since the first post bleach. @@ -172,7 +178,7 @@ public static Expression fitRecovery_diffOnly(double[] time, double[] normalized double bleachWhileMonitoringRate = inputparam[0]; modelExp = modelExp.getSubstitutedExpression(new Expression(FRAPDataAnalysis.symbol_bwmRate), new Expression(bleachWhileMonitoringRate)); Parameter parameters[] = new Parameter[] {FRAPDataAnalysis.para_If, FRAPDataAnalysis.para_Io, FRAPDataAnalysis.para_tau}; - modelExp.bindExpression(new SimpleSymbolTable(new String[] { "t", FRAPDataAnalysis.para_If.getName(), FRAPDataAnalysis.para_Io.getName(), FRAPDataAnalysis.para_tau.getName() })); + bindExpressionToParametersAndTime(modelExp, parameters); //estimate parameters by minimizing the errors between function values and reference data optResultSet = solve(modelExp.flatten(),parameters,normalized_time,normalized_fluor); @@ -262,14 +268,16 @@ public static double fitRecovery_reacKoffRateOnly(double[] time, double[][] norm if(fixedParameter == null) { + //get fitting parameter array + Parameter[] parameters = new Parameter[]{bwmParam, fittingParamA, koffParam}; //get expression pairs bwmRateExp = bwmRateExp.getSubstitutedExpression(new Expression(FRAPOptFunctions.SYMBOL_I_inicell), new Expression(inputparam[0])); + bindExpressionToParametersAndTime(bwmRateExp, parameters); ExplicitFitObjectiveFunction.ExpressionDataPair bwmRateExpDataPair = new ExplicitFitObjectiveFunction.ExpressionDataPair(bwmRateExp, 1); koffRateExp = koffRateExp.getSubstitutedExpression(new Expression(FRAPOptFunctions.SYMBOL_I_inibleached), new Expression(inputparam[1])); + bindExpressionToParametersAndTime(koffRateExp, parameters); ExplicitFitObjectiveFunction.ExpressionDataPair koffRateExpDataPair = new ExplicitFitObjectiveFunction.ExpressionDataPair(koffRateExp, 2); ExplicitFitObjectiveFunction.ExpressionDataPair[] expDataPairs = new ExplicitFitObjectiveFunction.ExpressionDataPair[]{bwmRateExpDataPair, koffRateExpDataPair}; - //get fitting parameter array - Parameter[] parameters = new Parameter[]{bwmParam, fittingParamA, koffParam}; //solve optResultSet = solve(expDataPairs, parameters, normalized_time, normalized_data, columnNames, weights); @@ -278,30 +286,34 @@ public static double fitRecovery_reacKoffRateOnly(double[] time, double[][] norm { if(fixedParameter != null && fixedParameter.getName().equals(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_BLEACH_MONITOR_RATE])) { + //get fitting parameter array + Parameter[] parameters = new Parameter[]{fittingParamA, koffParam}; //get expression pairs bwmRateExp = bwmRateExp.getSubstitutedExpression(new Expression(FRAPOptFunctions.SYMBOL_I_inicell), new Expression(inputparam[0])); bwmRateExp = bwmRateExp.getSubstitutedExpression(new Expression(FRAPOptFunctions.SYMBOL_BWM_RATE), new Expression(fixedParameter.getInitialGuess())); + bindExpressionToParametersAndTime(bwmRateExp, parameters); ExplicitFitObjectiveFunction.ExpressionDataPair bwmRateExpDataPair = new ExplicitFitObjectiveFunction.ExpressionDataPair(bwmRateExp, 1); koffRateExp = koffRateExp.getSubstitutedExpression(new Expression(FRAPOptFunctions.SYMBOL_I_inibleached), new Expression(inputparam[1])); koffRateExp = koffRateExp.getSubstitutedExpression(new Expression(FRAPOptFunctions.SYMBOL_BWM_RATE), new Expression(fixedParameter.getInitialGuess())); + bindExpressionToParametersAndTime(koffRateExp, parameters); ExplicitFitObjectiveFunction.ExpressionDataPair koffRateExpDataPair = new ExplicitFitObjectiveFunction.ExpressionDataPair(koffRateExp, 2); ExplicitFitObjectiveFunction.ExpressionDataPair[] expDataPairs = new ExplicitFitObjectiveFunction.ExpressionDataPair[]{bwmRateExpDataPair, koffRateExpDataPair}; - //get fitting parameter array - Parameter[] parameters = new Parameter[]{fittingParamA, koffParam}; //solve optResultSet = solve(expDataPairs, parameters, normalized_time, normalized_data, columnNames, weights); } else if(fixedParameter != null && fixedParameter.getName().equals(FRAPModel.MODEL_PARAMETER_NAMES[FRAPModel.INDEX_OFF_RATE])) { + //get fitting parameter array + Parameter[] parameters = new Parameter[]{bwmParam, fittingParamA}; //get expression pairs bwmRateExp = bwmRateExp.getSubstitutedExpression(new Expression(FRAPOptFunctions.SYMBOL_I_inicell), new Expression(inputparam[0])); + bindExpressionToParametersAndTime(bwmRateExp, parameters); ExplicitFitObjectiveFunction.ExpressionDataPair bwmRateExpDataPair = new ExplicitFitObjectiveFunction.ExpressionDataPair(bwmRateExp, 1); koffRateExp = koffRateExp.getSubstitutedExpression(new Expression(FRAPOptFunctions.SYMBOL_I_inibleached), new Expression(inputparam[1])); koffRateExp = koffRateExp.getSubstitutedExpression(new Expression(FRAPOptFunctions.SYMBOL_KOFF), new Expression(fixedParameter.getInitialGuess())); + bindExpressionToParametersAndTime(koffRateExp, parameters); ExplicitFitObjectiveFunction.ExpressionDataPair koffRateExpDataPair = new ExplicitFitObjectiveFunction.ExpressionDataPair(koffRateExp, 2); ExplicitFitObjectiveFunction.ExpressionDataPair[] expDataPairs = new ExplicitFitObjectiveFunction.ExpressionDataPair[]{bwmRateExpDataPair, koffRateExpDataPair}; - //get fitting parameter array - Parameter[] parameters = new Parameter[]{bwmParam, fittingParamA}; //solve optResultSet = solve(expDataPairs, parameters, normalized_time, normalized_data, columnNames, weights); } diff --git a/vcell-core/src/main/java/cbit/vcell/opt/ExplicitFitObjectiveFunction.java b/vcell-core/src/main/java/cbit/vcell/opt/ExplicitFitObjectiveFunction.java index b5a37600e4..76f6489104 100644 --- a/vcell-core/src/main/java/cbit/vcell/opt/ExplicitFitObjectiveFunction.java +++ b/vcell-core/src/main/java/cbit/vcell/opt/ExplicitFitObjectiveFunction.java @@ -48,16 +48,46 @@ public double f(double[] x) { double weightedSquaredErrors = 0; for (ExpressionDataPair pair : funcDataPairs){ double[] refData = simpleReferenceData.getDataByColumn(pair.referenceDataIndex); - double weight = simpleReferenceData.getColumnWeights()[pair.referenceDataIndex-1]; - for (int i=0;i