From 3fb82fe0fccc8c90c64d370a6afa231c503c32d9 Mon Sep 17 00:00:00 2001
From: "patrick.lambert" <patrick.mh.lambert@inrae.fr>
Date: Wed, 17 Feb 2021 19:02:53 +0100
Subject: [PATCH] possibility to export several outputs
---
exploration/R_AS_GR3D/tryFromRougier.R | 70 +++++-------------------
src/main/java/miscellaneous/EasyRun.java | 33 +++++++++--
2 files changed, 42 insertions(+), 61 deletions(-)
diff --git a/exploration/R_AS_GR3D/tryFromRougier.R b/exploration/R_AS_GR3D/tryFromRougier.R
index e793ccb..fc903b0 100644
--- a/exploration/R_AS_GR3D/tryFromRougier.R
+++ b/exploration/R_AS_GR3D/tryFromRougier.R
@@ -1,11 +1,9 @@
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)
-
-
diff --git a/src/main/java/miscellaneous/EasyRun.java b/src/main/java/miscellaneous/EasyRun.java
index 9333804..1beb5fd 100644
--- a/src/main/java/miscellaneous/EasyRun.java
+++ b/src/main/java/miscellaneous/EasyRun.java
@@ -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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