Commit 3fb82fe0 authored by patrick.lambert's avatar patrick.lambert
Browse files

possibility to export several outputs

parent 8285291e
library(rJava)
library(yaml)
#library(yaml)
library(dplyr)
rm(list=ls())
set.seed(1)
# # parameters and prios=rs of parameters to be fitted
# inputData = yaml.load_file("ABC_seq_2param_3stats_NewAfterSA.yaml")
# # load prior
......@@ -21,23 +19,25 @@ set.seed(1)
# }
# parametersNames = unlist(parametersNames)
parametersNames = c("processes.processesEachStep.8.tempMinRep",
"processes.processesEachStep.8.ratioS95_S50",
"processes.processesEachStep.6.pHomingAfterEquil")
thetas = c(10, 2, 0.7)
## to have the same working diretory as GR3D
setwd("../..")
# path to outputs
outputDir = "simus/"
jarfile = "../../target/GR3D-3.2-SNAPSHOT.jar"
jarfile = "target/GR3D-3.2-SNAPSHOT.jar"
simDuration = 48
simBegin = 1
timeStepDuration =1
seed = 1
## to have the same working diretory as GR3D
setwd("../..")
parametersNames = c("processes.processesEachStep.8.tempMinRep",
"processes.processesEachStep.8.ratioS95_S50",
"processes.processesEachStep.6.pHomingAfterEquil")
thetas = c(10, 2, 0.7)
arguments = c('','-simDuration',simDuration, '-simBegin',simBegin,
'-timeStepDuration',timeStepDuration,
......@@ -46,54 +46,12 @@ arguments = c('','-simDuration',simDuration, '-simBegin',simBegin,
'-env',"data/input/northeastamerica/RIOBNneaBasins_Rjava.xml",
'-observers',"data/input/northeastamerica/RIO_obs_empty.xml")
outputFile = paste0(outputDir,"output",seed)
outputFile = paste0("Avirer",seed)
.jinit(classpath = "", force.init = TRUE)
.jinit(classpath = jarfile, force.init = TRUE)
.jcall("miscellaneous.EasyRun","V","runSimulation",arguments, outputFile,.jarray(parametersNames),.jarray(thetas))
.jcall("miscellaneous.EasyRun","[D","getValuesFromEnvironement","getMeanLastPercOfAut")
.jcall("miscellaneous.EasyRun","[D","getValuesFromAquanismGroup","getRangeDistribution")
# return a function to run the model with parameters as arguments
salrun <- function(jarfile, simDuration, simBegin, timeStepDuration = 1) {
assign("inputData",inputData)
assign("outputDir",outputDir)
function(parameters) {
# loading the user's data
parametersNames = list()
for (i in 1:length(inputData$parameters)) {
parametersNames = c(parametersNames, inputData$parameters[[i]]$javapath)
}
# extracting the seed and the model parameters
seed=parameters[1]
thetas=parameters[2:length(parameters)]
outputFile = paste(outputDir,"output",seed,sep="")
if (!file.exists(paste(outputFile,".csv",sep=""))) {
# run
arguments=c('-q','-simDuration',simDuration, '-simBegin',simBegin,
'-timeStepDuration',timeStepDuration, '-groups',"data/input/fishTryRealBV_CC.xml",
'-env',"data/input/BNtryRealBasins.xml",'-observers',"data/input/obsTryRealABC.xml", '-RNGStatusIndex', format(seed,scientific=FALSE))
.jinit(classpath=jarfile)#, force.init=TRUE)
.jcall("miscellaneous.EasyABC","V","runSimulation",arguments, outputFile,.jarray(unlist(parametersNames)),.jarray(thetas))
}
# output
likelihood=as.double(as.matrix(read.csv(paste(outputFile,".csv",sep=""), skip=10, h=F, sep=";"))[1,2])
agestat=as.double(as.matrix(read.csv(paste(outputFile,".csv",sep=""), skip=11, h=F, sep=";"))[1,2])
maxlat=as.double(as.matrix(read.csv(paste(outputFile,".csv",sep=""), skip=12, h=F, sep=";"))[1,2])
if (maxlat>0)
c(likelihood,agestat,maxlat)
else
c(NA,NA,NA)
}
}
model = salrun(
jarfile = "GR3D-1.0-SNAPSHOT.jar",
simDuration = 400,
simBegin = 2)
......@@ -16,26 +16,36 @@
*/
package miscellaneous;
import java.util.Arrays;
import fr.cemagref.simaqualife.extensions.pilot.BatchRunner;
import fr.cemagref.simaqualife.pilot.Pilot;
public class EasyRun {
static Pilot pilot;
public static void runSimulation(String[] batchArgs, String outputfilename, String[] paramNames, double[] paramValues)
throws Exception {
try {
Pilot pilot = new Pilot();
pilot = new Pilot();
BatchRunner runner = new BatchRunner(pilot);
pilot.init();
runner.parseArgs(batchArgs, false, true, false);
pilot.load();
// update the simulation parameters
ReflectUtils.setFieldValueFromPath(pilot.getAquaticWorld().getAquaNismsGroupsList().get(0),
"processes.processesAtEnd.0.fileNameOutput", outputfilename);
for (int i = 0; i < paramNames.length; i++) {
ReflectUtils.setFieldValueFromPath(pilot.getAquaticWorld().getAquaNismsGroupsList().get(0), paramNames[i],
paramValues[i]);
}
// run the simulation
pilot.run();
// For forcing resources releasing (like shp files)
System.gc();
} catch (Throwable e) {
......@@ -45,6 +55,16 @@ public class EasyRun {
}
public static double[] getValuesFromEnvironement(String outputName) throws Exception {
return (double[]) ReflectUtils.getValueFromPath(pilot.getAquaticWorld().getEnvironment(), outputName);
}
public static double[] getValuesFromAquanismGroup(String outputName) throws Exception {
return (double[]) ReflectUtils.getValueFromPath(pilot.getAquaticWorld().getAquaNismsGroupsList().get(0), outputName);
}
public static void main(String[] args) throws Exception {
String[] batchArguments = ("-simDuration 48 -simBegin 1 -timeStepDuration 1 -RNGStatusIndex 1 "
+ "-groups data/input/northeastamerica/fishRIOBasin_Sapidissima_Rjava.xml "
......@@ -55,12 +75,15 @@ public class EasyRun {
"processes.processesEachStep.8.ratioS95_S50", "processes.processesEachStep.6.pHomingAfterEquil" };
double[] parameterValues = new double[] { 10, 2, 0.7 };
runSimulation(batchArguments, "tsointsoin", parameterNames, parameterValues);
// runSimulation(
// batchArguments, "data/output/tsointsoin", new String[] { " = c("processes.processesEachStep.8.tempMinRep"",
// "processes.processesEachStep.8.ratioS95_S50", "processes.processesEachStep.6.pHomingAfterEquil" },
// new double[] { 10, 2, 0.7 });
System.out.println(Arrays.toString(getValuesFromEnvironement("getMeanLastPercOfAut")));
System.out.println(Arrays.toString(getValuesFromAquanismGroup("getRangeDistribution")));
// double[] basinRecruitments = runSimulation(batchArguments, "tsointsoin", parameterNames, parameterValues);
// System.out.println(Arrays.toString(basinRecruitments));
}
}
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