V2_3.java [src/java/m/ghg/daycent] Revision: default Date:
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package m.ghg.daycent;
import csip.Config;
import csip.api.server.Executable;
import csip.api.client.ModelDataServiceCall;
import csip.api.server.PayloadParameter;
import csip.api.server.ServiceException;
import csip.SessionLogger;
import csip.annotations.Description;
import csip.annotations.Name;
import csip.annotations.Options;
import csip.annotations.Resource;
import csip.cosu.ObjFunc;
import csip.utils.Client;
import csip.utils.Parallel;
import gisobjects.GISObject;
import gisobjects.GISObjectFactory;
import gisobjects.db.GISEngineFactory;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
import java.nio.file.StandardOpenOption;
import java.sql.Connection;
import java.time.LocalDate;
import java.time.format.DateTimeFormatter;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Calendar;
import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Scanner;
import java.util.Set;
import java.util.logging.Level;
import java.util.logging.Logger;
import java.util.stream.Collectors;
import java.util.stream.DoubleStream;
import java.util.stream.IntStream;
import javax.ws.rs.Path;
import m.ghg.ApplicationResources;
import static m.ghg.ApplicationResources.*;
import static m.ghg.daycent.V1_0.ppdf3Def;
import static m.ghg.daycent.V1_0.ppdf4Def;
import static m.ghg.daycent.V1_0.pramxDef;
import oms3.ObjectiveFunction;
import org.codehaus.jettison.json.JSONArray;
import org.codehaus.jettison.json.JSONException;
import org.codehaus.jettison.json.JSONObject;
import util.DateConversion;
import util.ServiceUtils;
import util.ObjFuncs.*;
import static util.ServiceUtils.getStringColumnData;
/**
*
* @author sidereus, od
*/
@Name("Daycent simulation execution")
@Description("Daycent CSIP service")
@Path("m/daycent/2.3")
@Options(timeout = "PT10M")
@Resource(from = ApplicationResources.class)
public class V2_3 extends V1_0 {
static final Map<String, Double> yieldConv = new HashMap<>();
// slice by time (start and end) and convert it
/*
Corn: grams/square meter C to corn bushels per acre: cgracc value * 0.41652
Factor: 8.92179 / 0.45 / (56 * 0.85) = 0.41652
Soybean: cgracc value * 0.37982 bu/acre
Factor: 8.92179 / 0.45 / (60 * 0.87) = 0.37982
Wheat: cgracc value * 0.38200 bu/acre
Factor: 8.92179 / 0.45 / (60 * 0.865) = 0.38200
Oats: cgracc value * 0.72043 bu/acre
Factor: 8.92179 / 0.45 / (32 * 0.86) = 0.72043
Sorghum: cgracc value * 0.40694 bu/ac
Factor: 8.92179 / 0.45 / (56 * 0.87) = 0.38200
Sorghum Silage: cgracc value * 0.0124903 tons/acre
Factor: 0.00404686 Mg/ac / 0.45 C fraction / 0.72 dry fraction = 0.0124903 Mg/ac
Alfalfa Hay: cgracc value * 0. 0051275 tons/acre
Factor: 0.0044609 / 0.45 / 0.87 = 0.011394
Corn Silage: cgracc value * 0. 0118957 tons/acre
Factor: 0.0044609 / 0.45 / 0.375 = 0.026434
Sorghum Forage: cgracc value * 0. 0124903 tons/acre
Barley: cgracc value * 0.48594 bu/acre
Rice: cgracc value * 0.5507
Factor: 8.92179 / 0.45 / (45 * 0.8) = 0.5507
Sugar beet: cgracc value * 0.04956
Factor: 0.0044609 / 0.45 / 0.2 = 0.04956
https://catalog.extension.oregonstate.edu/em9324/html
*/
static {
yieldConv.put("C1", 0.41652);
yieldConv.put("C3", 0.41652);
yieldConv.put("C5", 0.41652);
yieldConv.put("C7", 0.41652);
yieldConv.put("C9", 0.41652);
yieldConv.put("C10", 0.41652);
yieldConv.put("C11", 0.41652);
yieldConv.put("C12", 0.41652);
yieldConv.put("C13", 0.41652);
yieldConv.put("PC13", 22.98690); // lbs/A 13.75% moisture
yieldConv.put("SC13", 79.30471); // lbs/A 75% moisture
yieldConv.put("SYBN1", 0.37982);
yieldConv.put("SYBN2", 0.37982);
yieldConv.put("SYBN3", 0.37982);
yieldConv.put("SYBN4", 0.37982);
yieldConv.put("BKW", 0.4539); // bu/ac 16% moisture
yieldConv.put("OAT1", 0.72043); // bu/ac 14% moisture
yieldConv.put("OAT2", 0.72043); // bu/ac 14% moisture
yieldConv.put("OAT3", 0.72043); // bu/ac 14% moisture
yieldConv.put("W1", 0.38200); // bu/ac 13.5% moisture
yieldConv.put("W2", 0.38200); // bu/ac 13.5% moisture
yieldConv.put("W3", 0.38200); // bu/ac 13.5% moisture
yieldConv.put("W4", 0.38200); // bu/ac 13.5% moisture
yieldConv.put("WSL4", 0.026435); // tons/ac 62.5% moisture
yieldConv.put("SW3", 0.38200); // bu/ac 13.5% moisture
yieldConv.put("SWSL4", 0.026435); // tons/ac 62.5% moisture
yieldConv.put("WBL4", 0.028323); // tons/ac 40% moisture
yieldConv.put("SW3P", 0.38200); // bu/ac 13.5% moisture
yieldConv.put("SW4", 0.38200); // bu/ac 13.5% moisture
yieldConv.put("SORG3", 0.40694); // bu/ac 13% moisture
yieldConv.put("FSORG", 0.012089); // hay short tons/ac 18% moisture
yieldConv.put("BSORG", 0.019826); // tons/ac 50% moisture
yieldConv.put("SSORG", 0.028323); // tons/ac 65% moisture
yieldConv.put("ALF1", 0.011394); // short tons/ac 13% moisture
yieldConv.put("ALF2", 0.011394); // short tons/ac 13% moisture
yieldConv.put("ALF3", 0.011394); // short tons/ac 13% moisture
yieldConv.put("ALF4", 0.011394); // short tons/ac 13% moisture
yieldConv.put("ALFB", 0.022029); // short tons/ac 55% moisture
yieldConv.put("G3CPI", 0.011394); // tons/ac
yieldConv.put("CSL9", 0.026435); // tons/ac 62.5% moisture
yieldConv.put("CSL10", 0.026435); // tons/ac 62.5% moisture
yieldConv.put("CSL11", 0.026435); // tons/ac 62.5% moisture
yieldConv.put("CSL12", 0.026435); // tons/ac 62.5% moisture
yieldConv.put("CSL13", 0.026435); // tons/ac 62.5% moisture
yieldConv.put("JTOM", 1.770197);
yieldConv.put("SUN", 21.9074); // lbs/ac 9.5% moisture
yieldConv.put("COT", 8.1812); // lbs/ac 7.5% moisture * 0.3817 since reported cotton yields in lbs/ac fiber from Truterra
yieldConv.put("COT2", 8.1812); // lbs/ac 7.5% moisture * 0.3817 since reported cotton yields in lbs/ac fiber from Truterra
yieldConv.put("BAR3", 0.46937); // bu/ac 12% moisture
yieldConv.put("TRIT", 0.42445); // triticale bu/ac 13.5% moisture
yieldConv.put("RYE", 0.40929); // rye bu/ac 13% moisture
yieldConv.put("RSIL", 0.02832);// ton/ac 65% moisture for silage
yieldConv.put("RHAY", 0.01983);// currently ton/ac 50% moisture for hay
yieldConv.put("BSIL", 0.02832);// ton/ac 65% moisture for silage
yieldConv.put("DBEAN", 23.603); // bu/ac 16% moisture
yieldConv.put("MBEAN", 22.5298); // lbs/ac 12% moisture
yieldConv.put("PEA", 23.60262); // lbs/ac 16% moisture content
yieldConv.put("PNUT", 22.15225); //
// yieldConv.put("CLV1", 23.325);
yieldConv.put("CLV1", 0.0116625); // 15% moisture clover in tons/A
yieldConv.put("LENT", 23.05372); // lbs/ac 14% moisture
yieldConv.put("SAFF", 22.65851); // lbs/ac canola
yieldConv.put("RICL", 0.50642); // bu/ac 13% moisture
yieldConv.put("SUGB", 0.033044); // short tons/ac 30% moisture content
yieldConv.put("CHAY", 0.01208916); // tons/ac 18% moisture content
yieldConv.put("MS", 21.9074); // lbs/ac 9.5% moisture content
}
protected JSONObject rotation;
protected List<Integer> crop_id;
protected Collection<String> JSONparams;
protected Integer cokey;
protected Double area;
protected Integer yearPractChange;
protected Integer staticYearPractChange = 2011;
protected Integer endPractChange;
protected Integer projectionYear;
protected Double nodata;
protected Boolean calibonly;
protected int colGracc = 0;
protected int colAgcacc = 0;
protected int colAbove = 0;
protected int colBelowFineRoots = 0;
protected int colBelowMatureRoots = 0;
protected int colSOM = 0;
protected String lrr = null;
@Override
protected void preProcess() throws ServiceException {
schedule = parameter().getString(SCHEDULE_FILE);
schedule_IC = parameter().getString(SCHEDULE_FILE_IC, "");
useClimateWind = parameter().getBoolean(USE_CLIMATE_WIND, false);
fileAsJSON = parameter().getBoolean(STREAM_FILE, false);
weatherDuration = parameter().getInt(WEATHER_DURATION_TXT);
startingYear = parameter().getInt(STARTING_YEAR_TXT);
schedule = ServiceUtils.checkRemoveExtension(schedule);
aoa_geometry = parameter().getJSON(soils.AoA.AOA_GEOMETRY);
cokey = parameter().getInt("cokey");
area = parameter().getDouble("area");
yearPractChange = parameter().getInt("yearPractChange");
endPractChange = parameter().getInt("endPractChange", 2020);
projectionYear = parameter().getInt("projectionYear", 2030);
calibonly = parameter().getBoolean("calibration");
nodata = parameter().getDouble("nodata", -9999.0);
JSONparams = parameter().getNames();
}
private void createCopy(String original, String copy) {
String sourcePath = workspace().getFile(original).getAbsolutePath();
String destPath = workspace().getDir().getAbsolutePath()
.concat(File.separator).concat(copy);
File sourceTemplate = new File(sourcePath);
File destTemplate = new File(destPath);
try {
Files.copy(sourceTemplate.toPath(), destTemplate.toPath());
} catch (IOException ex) {
throw new RuntimeException(ex.getMessage());
}
}
protected void fetchClimate(int startYear, int duration, String outputfile, Integer counter) throws JSONException, Exception {
ModelDataServiceCall mds = new ModelDataServiceCall()
.put(STARTING_YEAR_TXT, startYear)
.put(WEATHER_DURATION_TXT, duration) // 10 ears for 2030 projection
.put(STREAM_FILE, fileAsJSON)
.put(USE_CLIMATE_WIND, useClimateWind)
.put(soils.AoA.AOA_GEOMETRY, new JSONObject()
.put(TYPE, aoa_geometry.get(TYPE))
.put(COORDINATES, aoa_geometry.get(COORDINATES)))
.url(Config.getString(WEATHER_URL_KEY,
request().getCodebase() + "d/weather/cligen/1.0"))
.withRetryPause(1000)
.withRetries(10) // 10 retries for climate to avoid failures
.call();
if (mds.serviceFinished()) {
mds.download(DAYCENT_WEATHER, workspace().getFile(outputfile));
} else if (counter != null && counter.equals(10)) {
throw new ServiceException("GHG Weather service error: " + mds.getError());
} else {
if (counter == null) {
counter = 1;
} else {
counter++;
}
LOG.info("Climate service call Counter: " + counter);
fetchClimate(startYear, duration, outputfile, counter);
}
}
private String getLRR(JSONArray centroid) throws Exception {
ModelDataServiceCall res = new ModelDataServiceCall()
.put("assessment_location", "Point", centroid)
.url(LRR_URL)
.withDefaultLogger()
.call();
String zone;
if (res.serviceFinished()) {
zone = res.getString("lrrsym");
} else {
String msg = res.getError();
throw new RuntimeException(msg);
}
return zone;
}
@Override
protected void doProcess() throws Exception {
// Get centroid of shape, if it is not a point already. (If it's a point, the centroid is the point)
try (Connection conn = resources().getJDBC(GISDB_SQLSVR)) {
GISObject shape = GISObjectFactory.createGISObject(aoa_geometry, GISEngineFactory.createGISEngine(conn));
// getLat/Lon functions get point value or the centroid of the shape.
latlon[0] = shape.getLatitude();
latlon[1] = shape.getLongitude();
}
JSONArray centroid = new JSONArray();
centroid.put(latlon[1]);
centroid.put(latlon[0]);
lrr = getLRR(centroid);
createCopy("fix.100", "fix_2.100");
createCopy("sitepar.in", "sitepar_2.in");
// if (lrr.toLowerCase().equals("c") ||
// lrr.toLowerCase().equals("r")) {
// createCopy("fix.100", "fix_3.100");
// createCopy("sitepar.in", "sitepar_3.in");
// }
getJSONParams();
Parallel.run(Config.getBoolean("ghg.serial.datafetch", false),
() -> {
int duration = endPractChange - 1979;
fetchClimate(1979, duration, "dayCentWeather.IN", null);
computeWeatherStats();
},
() -> {
fetchSoil(calibonly, null);
countLayers(); // testing if we need the fix structure in Black et al. 2017
},
() -> {
int duration = endPractChange - 2010;
fetchClimate(2010, duration, "dayCentW2030.IN", null);
}
);
if (!sitepars.isEmpty()) {
if (sitepars.get("site").containsKey("pa_dmpflux")) {
double val = sitepars.get("site").get("pa_dmpflux");
sitepars.get("site").put("dmpflux", val);
}
if (sitepars.get("site").containsKey("pa_MaxNitAmt")) {
double val = sitepars.get("site").get("pa_MaxNitAmt");
sitepars.get("site").put("MaxNitAmt", val);
}
if (sitepars.get("site").containsKey("pa_wfpsdnitadj")) {
double val = sitepars.get("site").get("pa_wfpsdnitadj");
sitepars.get("site").put("wfpsdnitadj", val);
}
if (sitepars.get("site").containsKey("pa_n2n2oadj")) {
double val = sitepars.get("site").get("pa_n2n2oadj");
sitepars.get("site").put("n2n2oadj", val);
}
}
if (!fixes.isEmpty()) {
if (fixes.get("fixes").containsKey("pa_dec52")) {
double val = fixes.get("fixes").get("pa_dec52");
fixes.get("fixes").put("dec52", val);
}
if (fixes.get("fixes").containsKey("pa_dec11")) {
double val = fixes.get("fixes").get("pa_dec11");
fixes.get("fixes").put("dec11", val);
}
if (fixes.get("fixes").containsKey("pa_dec12")) {
double val = fixes.get("fixes").get("pa_dec12");
fixes.get("fixes").put("dec12", val);
}
if (fixes.get("fixes").containsKey("pa_dec21")) {
double val = fixes.get("fixes").get("pa_dec21");
fixes.get("fixes").put("dec21", val);
}
if (fixes.get("fixes").containsKey("pa_dec22")) {
double val = fixes.get("fixes").get("pa_dec22");
fixes.get("fixes").put("dec22", val);
}
if (fixes.get("fixes").containsKey("pa_dec31")) {
double val = fixes.get("fixes").get("pa_dec31");
fixes.get("fixes").put("dec31", val);
}
if (fixes.get("fixes").containsKey("pa_dec51")) {
double val = fixes.get("fixes").get("pa_dec51");
fixes.get("fixes").put("dec51", val);
}
if (fixes.get("fixes").containsKey("pa_dec4")) {
double val = fixes.get("fixes").get("pa_dec4");
fixes.get("fixes").put("dec4", val);
}
if (fixes.get("fixes").containsKey("pa_dec32")) {
double val = fixes.get("fixes").get("pa_dec32");
fixes.get("fixes").put("dec32", val);
}
if (fixes.get("fixes").containsKey("pa_teff1")) {
double val = fixes.get("fixes").get("pa_teff1");
fixes.get("fixes").put("teff1", val);
}
if (fixes.get("fixes").containsKey("pa_teff2")) {
double val = fixes.get("fixes").get("pa_teff2");
fixes.get("fixes").put("teff2", val);
}
if (fixes.get("fixes").containsKey("pa_teff3")) {
double val = fixes.get("fixes").get("pa_teff3");
fixes.get("fixes").put("teff3", val);
}
if (fixes.get("fixes").containsKey("pa_teff4")) {
double val = fixes.get("fixes").get("pa_teff4");
fixes.get("fixes").put("teff4", val);
}
if (fixes.get("fixes").containsKey("pa_ps1s31")) {
double val = fixes.get("fixes").get("pa_ps1s31");
fixes.get("fixes").put("ps1s31", val);
}
if (fixes.get("fixes").containsKey("pa_ps1s32")) {
double val = fixes.get("fixes").get("pa_ps1s32");
fixes.get("fixes").put("ps1s32", val);
}
if (fixes.get("fixes").containsKey("pa_ps2s31")) {
double val = fixes.get("fixes").get("pa_ps2s31");
fixes.get("fixes").put("ps2s31", val);
}
if (fixes.get("fixes").containsKey("pa_ps2s32")) {
double val = fixes.get("fixes").get("pa_ps2s32");
fixes.get("fixes").put("ps2s32", val);
}
if (fixes.get("fixes").containsKey("pa_fleach3")) {
double val = fixes.get("fixes").get("pa_fleach3");
fixes.get("fixes").put("fleach3", val);
}
if (fixes.get("fixes").containsKey("pa_pmco22")) {
double val = fixes.get("fixes").get("pa_pmco22");
fixes.get("fixes").put("pmco22", val);
}
if (fixes.get("fixes").containsKey("pa_p2co22")) {
double val = fixes.get("fixes").get("pa_p2co22");
fixes.get("fixes").put("p2co22", val);
}
if (fixes.get("fixes").containsKey("pa_ps1co22")) {
double val = fixes.get("fixes").get("pa_ps1co22");
fixes.get("fixes").put("ps1co22", val);
}
if (fixes.get("fixes").containsKey("pa_p1co2a2")) {
double val = fixes.get("fixes").get("pa_p1co2a2");
fixes.get("fixes").put("p1co2a2", val);
}
if (fixes.get("fixes").containsKey("pa_p1co2b2")) {
double val = fixes.get("fixes").get("pa_p1co2b2");
fixes.get("fixes").put("p1co2b2", val);
}
if (fixes.get("fixes").containsKey("pa_p3co2")) {
double val = fixes.get("fixes").get("pa_p3co2");
fixes.get("fixes").put("p3co2", val);
}
}
// RENAME PRE-AG SCH
java.nio.file.Path source = workspace().getFile("pa_Truterra.sch").toPath();
Files.move(source, source.resolveSibling("Truterra.sch"), StandardCopyOption.REPLACE_EXISTING);
createConfig("crop.100");
createConfig(getSite100());
createConfig("fix.100"); // values from payload _pa
createConfig("sitepar.in");
createConfig("soils.in");
createConfig("tree.100");
runDaycent();
runDaycentList();
source = workspace().getFile("Truterra.sch").toPath();
Files.move(source, source.resolveSibling("Truterra_pa.sch"), StandardCopyOption.REPLACE_EXISTING);
java.nio.file.Path sourceBin = workspace().getFile("Truterra.bin").toPath();
Files.move(sourceBin, sourceBin.resolveSibling("Truterra_pa.bin"), StandardCopyOption.REPLACE_EXISTING);
java.nio.file.Path sourceFix = workspace().getFile("fix.100").toPath();
Files.move(sourceFix, sourceFix.resolveSibling("fix_pa.100"), StandardCopyOption.REPLACE_EXISTING);
sourceFix = workspace().getFile("fix_2.100").toPath();
Files.move(sourceFix, sourceFix.resolveSibling("fix.100"), StandardCopyOption.REPLACE_EXISTING);
java.nio.file.Path sourceSite = workspace().getFile("sitepar.in").toPath();
Files.move(sourceSite, sourceSite.resolveSibling("sitepar_pa.in"), StandardCopyOption.REPLACE_EXISTING);
sourceSite = workspace().getFile("sitepar_2.in").toPath();
Files.move(sourceSite, sourceSite.resolveSibling("sitepar.in"), StandardCopyOption.REPLACE_EXISTING);
java.nio.file.Path sourceLis = workspace().getFile("Truterra.lis").toPath();
Files.move(sourceLis, sourceLis.resolveSibling("Truterra_pa.lis"), StandardCopyOption.REPLACE_EXISTING);
java.nio.file.Path outfiles = workspace().getFile("outfiles.in").toPath();
Files.move(outfiles, outfiles.resolveSibling("outfiles_pa.in"), StandardCopyOption.REPLACE_EXISTING);
outfiles = workspace().getFile("outfiles_ag.in").toPath();
Files.move(outfiles, outfiles.resolveSibling("outfiles.in"), StandardCopyOption.REPLACE_EXISTING);
Files.delete(workspace().getFile("year_summary.out").toPath());
if (!sitepars.isEmpty()) {
if (sitepars.get("site").containsKey("ag_dmpflux")) {
double val = sitepars.get("site").get("ag_dmpflux");
sitepars.get("site").put("dmpflux", val);
}
if (sitepars.get("site").containsKey("ag_MaxNitAmt")) {
double val = sitepars.get("site").get("ag_MaxNitAmt");
sitepars.get("site").put("MaxNitAmt", val);
}
if (sitepars.get("site").containsKey("ag_wfpsdnitadj")) {
double val = sitepars.get("site").get("ag_wfpsdnitadj");
sitepars.get("site").put("wfpsdnitadj", val);
}
if (sitepars.get("site").containsKey("ag_n2n2oadj")) {
double val = sitepars.get("site").get("ag_n2n2oadj");
sitepars.get("site").put("n2n2oadj", val);
}
}
if (!fixes.isEmpty()) {
if (fixes.get("fixes").containsKey("ag_dec52")) {
double val = fixes.get("fixes").get("ag_dec52");
fixes.get("fixes").put("dec52", val);
}
if (fixes.get("fixes").containsKey("ag_dec11")) {
double val = fixes.get("fixes").get("ag_dec11");
fixes.get("fixes").put("dec11", val);
}
if (fixes.get("fixes").containsKey("ag_dec12")) {
double val = fixes.get("fixes").get("ag_dec12");
fixes.get("fixes").put("dec12", val);
}
if (fixes.get("fixes").containsKey("ag_dec22")) {
double val = fixes.get("fixes").get("ag_dec22");
fixes.get("fixes").put("dec22", val);
}
if (fixes.get("fixes").containsKey("ag_dec21")) {
double val = fixes.get("fixes").get("ag_dec21");
fixes.get("fixes").put("dec21", val);
}
if (fixes.get("fixes").containsKey("ag_dec31")) {
double val = fixes.get("fixes").get("ag_dec31");
fixes.get("fixes").put("dec31", val);
}
if (fixes.get("fixes").containsKey("ag_dec51")) {
double val = fixes.get("fixes").get("ag_dec51");
fixes.get("fixes").put("dec51", val);
}
if (fixes.get("fixes").containsKey("ag_dec4")) {
double val = fixes.get("fixes").get("ag_dec4");
fixes.get("fixes").put("dec4", val);
}
if (fixes.get("fixes").containsKey("ag_dec32")) {
double val = fixes.get("fixes").get("ag_dec32");
fixes.get("fixes").put("dec32", val);
}
if (fixes.get("fixes").containsKey("ag_teff1")) {
double val = fixes.get("fixes").get("ag_teff1");
fixes.get("fixes").put("teff1", val);
}
if (fixes.get("fixes").containsKey("ag_teff2")) {
double val = fixes.get("fixes").get("ag_teff2");
fixes.get("fixes").put("teff2", val);
}
if (fixes.get("fixes").containsKey("ag_teff3")) {
double val = fixes.get("fixes").get("ag_teff3");
fixes.get("fixes").put("teff3", val);
}
if (fixes.get("fixes").containsKey("ag_teff4")) {
double val = fixes.get("fixes").get("ag_teff4");
fixes.get("fixes").put("teff4", val);
}
if (fixes.get("fixes").containsKey("ag_ps1s31")) {
double val = fixes.get("fixes").get("ag_ps1s31");
fixes.get("fixes").put("ps1s31", val);
}
if (fixes.get("fixes").containsKey("ag_ps1s32")) {
double val = fixes.get("fixes").get("ag_ps1s32");
fixes.get("fixes").put("ps1s32", val);
}
if (fixes.get("fixes").containsKey("ag_ps2s31")) {
double val = fixes.get("fixes").get("ag_ps2s31");
fixes.get("fixes").put("ps2s31", val);
}
if (fixes.get("fixes").containsKey("ag_ps2s32")) {
double val = fixes.get("fixes").get("ag_ps2s32");
fixes.get("fixes").put("ps2s32", val);
}
if (fixes.get("fixes").containsKey("ag_fleach3")) {
double val = fixes.get("fixes").get("ag_fleach3");
fixes.get("fixes").put("fleach3", val);
}
if (fixes.get("fixes").containsKey("ag_pmco22")) {
double val = fixes.get("fixes").get("ag_pmco22");
fixes.get("fixes").put("pmco22", val);
}
if (fixes.get("fixes").containsKey("ag_p2co22")) {
double val = fixes.get("fixes").get("ag_p2co22");
fixes.get("fixes").put("p2co22", val);
}
if (fixes.get("fixes").containsKey("ag_ps1co22")) {
double val = fixes.get("fixes").get("ag_ps1co22");
fixes.get("fixes").put("ps1co22", val);
}
if (fixes.get("fixes").containsKey("ag_p1co2a2")) {
double val = fixes.get("fixes").get("ag_p1co2a2");
fixes.get("fixes").put("p1co2a2", val);
}
if (fixes.get("fixes").containsKey("ag_p1co2b2")) {
double val = fixes.get("fixes").get("ag_p1co2b2");
fixes.get("fixes").put("p1co2b2", val);
}
if (fixes.get("fixes").containsKey("ag_p3co2")) {
double val = fixes.get("fixes").get("ag_p3co2");
fixes.get("fixes").put("p3co2", val);
}
}
// RENAME AG SCH
source = workspace().getFile("ag_Truterra.sch").toPath();
Files.move(source, source.resolveSibling("Truterra.sch"), StandardCopyOption.REPLACE_EXISTING);
createConfig("fix.100"); // values from payload _ag
createConfig("sitepar.in");
schedule_IC = "Truterra_pa.bin";
runDaycent();
runDaycentList();
// if (lrr.toLowerCase().equals("c") ||
// lrr.toLowerCase().equals("r")) {
// source = workspace().getFile("Truterra.sch").toPath();
// Files.move(source, source.resolveSibling("Truterra_ag.sch"), StandardCopyOption.REPLACE_EXISTING);
//
// sourceBin = workspace().getFile("Truterra.bin").toPath();
// Files.move(sourceBin, sourceBin.resolveSibling("Truterra_ag.bin"), StandardCopyOption.REPLACE_EXISTING);
//
// sourceFix = workspace().getFile("fix.100").toPath();
// Files.move(sourceFix, sourceFix.resolveSibling("fix_ag.100"), StandardCopyOption.REPLACE_EXISTING);
//
// sourceFix = workspace().getFile("fix_3.100").toPath();
// Files.move(sourceFix, sourceFix.resolveSibling("fix.100"), StandardCopyOption.REPLACE_EXISTING);
//
// sourceSite = workspace().getFile("sitepar.in").toPath();
// Files.move(sourceSite, sourceSite.resolveSibling("sitepar_ag.in"), StandardCopyOption.REPLACE_EXISTING);
//
// sourceSite = workspace().getFile("sitepar_3.in").toPath();
// Files.move(sourceSite, sourceSite.resolveSibling("sitepar.in"), StandardCopyOption.REPLACE_EXISTING);
//
// sourceLis = workspace().getFile("Truterra.lis").toPath();
// Files.move(sourceLis, sourceLis.resolveSibling("Truterra_ag.lis"), StandardCopyOption.REPLACE_EXISTING);
////
//// outfiles = workspace().getFile("outfiles.in").toPath();
//// Files.move(outfiles, outfiles.resolveSibling("outfiles_pa.in"), StandardCopyOption.REPLACE_EXISTING);
//// outfiles = workspace().getFile("outfiles_ag.in").toPath();
//// Files.move(outfiles, outfiles.resolveSibling("outfiles.in"), StandardCopyOption.REPLACE_EXISTING);
//
// Files.delete(workspace().getFile("year_summary.out").toPath());
//
// if (!sitepars.isEmpty()) {
// if (sitepars.get("site").containsKey("tt_dmpflux")) {
// double val = sitepars.get("site").get("tt_dmpflux");
// sitepars.get("site").put("dmpflux", val);
// }
// if (sitepars.get("site").containsKey("tt_MaxNitAmt")) {
// double val = sitepars.get("site").get("tt_MaxNitAmt");
// sitepars.get("site").put("MaxNitAmt", val);
// }
// if (sitepars.get("site").containsKey("tt_wfpsdnitadj")) {
// double val = sitepars.get("site").get("tt_wfpsdnitadj");
// sitepars.get("site").put("wfpsdnitadj", val);
// }
// if (sitepars.get("site").containsKey("tt_n2n2oadj")) {
// double val = sitepars.get("site").get("tt_n2n2oadj");
// sitepars.get("site").put("n2n2oadj", val);
// }
// }
//
// if (!fixes.isEmpty()) {
// if (fixes.get("fixes").containsKey("tt_dec52")) {
// double val = fixes.get("fixes").get("tt_dec52");
// fixes.get("fixes").put("dec52", val);
// }
// if (fixes.get("fixes").containsKey("tt_dec11")) {
// double val = fixes.get("fixes").get("tt_dec11");
// fixes.get("fixes").put("dec11", val);
// }
// if (fixes.get("fixes").containsKey("tt_dec12")) {
// double val = fixes.get("fixes").get("tt_dec12");
// fixes.get("fixes").put("dec12", val);
// }
// if (fixes.get("fixes").containsKey("tt_dec22")) {
// double val = fixes.get("fixes").get("tt_dec22");
// fixes.get("fixes").put("dec22", val);
// }
// if (fixes.get("fixes").containsKey("tt_dec21")) {
// double val = fixes.get("fixes").get("tt_dec21");
// fixes.get("fixes").put("dec21", val);
// }
// if (fixes.get("fixes").containsKey("tt_dec31")) {
// double val = fixes.get("fixes").get("tt_dec31");
// fixes.get("fixes").put("dec31", val);
// }
// if (fixes.get("fixes").containsKey("tt_dec51")) {
// double val = fixes.get("fixes").get("tt_dec51");
// fixes.get("fixes").put("dec51", val);
// }
// if (fixes.get("fixes").containsKey("tt_dec4")) {
// double val = fixes.get("fixes").get("tt_dec4");
// fixes.get("fixes").put("dec4", val);
// }
// if (fixes.get("fixes").containsKey("tt_dec32")) {
// double val = fixes.get("fixes").get("tt_dec32");
// fixes.get("fixes").put("dec32", val);
// }
// if (fixes.get("fixes").containsKey("tt_teff1")) {
// double val = fixes.get("fixes").get("tt_teff1");
// fixes.get("fixes").put("teff1", val);
// }
// if (fixes.get("fixes").containsKey("tt_teff2")) {
// double val = fixes.get("fixes").get("tt_teff2");
// fixes.get("fixes").put("teff2", val);
// }
// if (fixes.get("fixes").containsKey("tt_teff3")) {
// double val = fixes.get("fixes").get("tt_teff3");
// fixes.get("fixes").put("teff3", val);
// }
// if (fixes.get("fixes").containsKey("tt_teff4")) {
// double val = fixes.get("fixes").get("tt_teff4");
// fixes.get("fixes").put("teff4", val);
// }
// if (fixes.get("fixes").containsKey("tt_ps1s31")) {
// double val = fixes.get("fixes").get("tt_ps1s31");
// fixes.get("fixes").put("ps1s31", val);
// }
// if (fixes.get("fixes").containsKey("tt_ps1s32")) {
// double val = fixes.get("fixes").get("tt_ps1s32");
// fixes.get("fixes").put("ps1s32", val);
// }
// if (fixes.get("fixes").containsKey("tt_ps2s31")) {
// double val = fixes.get("fixes").get("tt_ps2s31");
// fixes.get("fixes").put("ps2s31", val);
// }
// if (fixes.get("fixes").containsKey("tt_ps2s32")) {
// double val = fixes.get("fixes").get("tt_ps2s32");
// fixes.get("fixes").put("ps2s32", val);
// }
// if (fixes.get("fixes").containsKey("tt_fleach3")) {
// double val = fixes.get("fixes").get("tt_fleach3");
// fixes.get("fixes").put("fleach3", val);
// }
// if (fixes.get("fixes").containsKey("tt_pmco22")) {
// double val = fixes.get("fixes").get("tt_pmco22");
// fixes.get("fixes").put("pmco22", val);
// }
// if (fixes.get("fixes").containsKey("tt_p2co22")) {
// double val = fixes.get("fixes").get("tt_p2co22");
// fixes.get("fixes").put("p2co22", val);
// }
// if (fixes.get("fixes").containsKey("tt_ps1co22")) {
// double val = fixes.get("fixes").get("tt_ps1co22");
// fixes.get("fixes").put("ps1co22", val);
// }
// if (fixes.get("fixes").containsKey("tt_p1co2a2")) {
// double val = fixes.get("fixes").get("tt_p1co2a2");
// fixes.get("fixes").put("p1co2a2", val);
// }
// if (fixes.get("fixes").containsKey("tt_p1co2b2")) {
// double val = fixes.get("fixes").get("tt_p1co2b2");
// fixes.get("fixes").put("p1co2b2", val);
// }
// if (fixes.get("fixes").containsKey("tt_p3co2")) {
// double val = fixes.get("fixes").get("tt_p3co2");
// fixes.get("fixes").put("p3co2", val);
// }
// }
//
// // RENAME AG SCH
// source = workspace().getFile("tt_Truterra.sch").toPath();
// Files.move(source, source.resolveSibling("Truterra.sch"), StandardCopyOption.REPLACE_EXISTING);
// createConfig("fix.100"); // values from payload _ag
// createConfig("sitepar.in");
// schedule_IC = "Truterra_ag.bin";
// runDaycent();
// runDaycentList();
//
// source = workspace().getFile("Truterra.sch").toPath();
// Files.move(source, source.resolveSibling("Truterra_tt.sch"), StandardCopyOption.REPLACE_EXISTING);
//
// File f = workspace().getFile("Truterra.sch");
// f.createNewFile();
// java.nio.file.Path p = workspace().getFile("Truterra.sch").toPath();
// java.nio.file.Path ag = workspace().getFile("Truterra_ag.sch").toPath();
// java.nio.file.Path tt = workspace().getFile("Truterra_tt.sch").toPath();
// List<String> ff = Files.readAllLines(tt);
// ff.remove(0);
// ff.remove(0);
// ff.remove(0);
// ff.remove(0);
// ff.remove(0);
// ff.remove(0);
// ff.remove(0);
// ff.remove(0);
// ff.remove(0);
// ff.remove(0);
// ff.remove(0);
// ff.remove(0);
// ff.remove(0);
// ff.remove(0);
// ff.remove(0);
// ff.remove(0);
// ff.remove(0);
// try (FileWriter fileWriter = new FileWriter(workspace().getFile("tt.sch"))) {
// for (String s : ff) {
// fileWriter.write(s + System.lineSeparator());
// }
// }
// java.nio.file.Path agg = workspace().getFile("tt.sch").toPath();
// Files.write(p, Files.readAllBytes(ag), StandardOpenOption.APPEND);
// Files.write(p, Files.readAllBytes(agg), StandardOpenOption.APPEND);
//
// }
// checkHarvest();
}
public static Map<Integer, Double> getMapFor(File wsFile, String column) throws IOException {
String[] time = getStringColumnData(wsFile, "time");
String[] col = getStringColumnData(wsFile, column);
return createlookup(time, col);
}
static Map<Integer, Double> createlookup(String[] key, String[] val) {
Map<Integer, Double> m = new LinkedHashMap<>();
for (int i = 0; i < val.length; i++) {
if (val[i].equals("-nan")) {
val[i] = "0.0"; // when CH4 is -nan
}
m.put(Double.valueOf(key[i]).intValue() - MODEL_OFFSET, Double.parseDouble(val[i]));
}
return m;
}
/* slice by time
*/
static Map<Integer, Double> slize(int start, int end, Map<Integer, Double> orig) {
return orig.entrySet()
.stream()
.filter(map -> map.getKey() >= start && map.getKey() <= end)
.collect(Collectors.toMap(map -> map.getKey(), map -> map.getValue()));
}
/* convert the value
*/
static Map<Integer, Double> convert(double factor, Map<Integer, Double> orig) {
return orig.entrySet()
.stream()
.collect(Collectors.toMap(map -> map.getKey(), map -> map.getValue() * factor));
}
void parseYearSummary() throws IOException {
File ys_out = workspace().getFile("year_summary.out");
Map<Integer, Double> N2Oflux = getMapFor(ys_out, "N2Oflux");
Map<Integer, Double> pcChangeN2Oflux = slize(yearPractChange, endPractChange, N2Oflux);
// N2O conversion: 1 g/m2 N2O-N = 1.895087 Mg/ac CO2e
Map<Integer, Double> conv_pcChangeN2Oflux = convert(1.895087, pcChangeN2Oflux);
double sumN2Oflux = conv_pcChangeN2Oflux.values().stream().mapToDouble(Double::doubleValue).sum();
Map<Integer, Double> CH4flux = getMapFor(ys_out, "CH4");
Map<Integer, Double> pcChangeCH4flux = slize(yearPractChange, endPractChange, CH4flux);
// CH4 conversion: 1 g/m2 CH4-C = 0.453248 Mg/ac CO2e
Map<Integer, Double> conv_pcChangeCH4flux = convert(0.453248, pcChangeCH4flux);
double sumCH4flux = conv_pcChangeCH4flux.values().stream().mapToDouble(Double::doubleValue).sum();
// put it into the result payload
results().put("N2O", sumN2Oflux);
results().put("CH4", sumCH4flux);
}
@Override
protected void postProcess() throws Exception {
// List<String> l = getRequestedObjfunc();
File ys_out = workspace().getFile("year_summary.out");
Map<Integer, Double> N2Oflux = getMapFor(ys_out, "N2Oflux");
Map<Integer, Double> CH4flux = getMapFor(ys_out, "CH4");
if (cosu().isRequested()) {
calibrate();
} else {
parseLis(N2Oflux, CH4flux);
// parseYearSummary();
}
}
//////////// Calibration
void calibrate() throws Exception {
for (String name : cosu().getNames()) {
String[] data = cosu().getData(name);
if (data.length != 2) {
throw new ServiceException("2 elements expected");
}
// this returns null is the OF is unknown.
ObjFunc of = cosu().getObjFunc(name);
// data[0] : calibration target (e.g. yield)
// data[1] : calibration details (startyear/endyear)
double v = calcObjFunc(of, LOG,
workspace().getFile("Truterra.sch"),
workspace().getFile("Truterra.lis"),
workspace().getFile("vswc.out"),
workspace().getFile("year_summary.out"),
data[0], data[1], nodata);
cosu().setValue(name, v);
}
}
//
// //////////// Calibration
// void calibrate(List<String> l) throws Exception {
// for (String ofName : l) {
//
// // 2 values
// String[] data = parameter().getStringArray(ofName);
// if (data.length != 2) {
// throw new ServiceException("Invalid of content, 2 elements expected");
// }
//
// // data[0] : calibration target (e.g. yield)
// // data[1] : calibration details (startyear/endyear)
// double v = calcObjFunc(LOG,
// workspace().getFile("Truterra.sch"),
// workspace().getFile("Truterra.lis"),
// data[0], data[1]);
// results().put(ofName, v);
// }
// }
static double[] getSimulatedOUT(SessionLogger LOG, File outfile, int column,
LocalDate starty, LocalDate endy, Double nodata) throws IOException, ServiceException {
// get the raw values from lis file: as map
// e.g. time -> cgracc
Map<String, String> c0_2 = ServiceUtils.getMapFor(outfile, column); // layer 1 0-2 cm
Map<String, String> c2_5 = ServiceUtils.getMapFor(outfile, column + 1); // layer 2 2-5 cm
Map<String, String> c5_10 = ServiceUtils.getMapFor(outfile, column + 2); // layer 3 5-10 cm
Map<String, String> c10_20 = ServiceUtils.getMapFor(outfile, column + 3); // layer 4 10-20 cm
Map<String, String> c20_30 = ServiceUtils.getMapFor(outfile, column + 4); // layer 5 20-30 cm
Map<String, String> c30_45 = ServiceUtils.getMapFor(outfile, column + 5); // layer 6 30-45 cm
Map<String, String> c45_60 = ServiceUtils.getMapFor(outfile, column + 6); // layer 7 45-60 cm
Map<String, String> c60_75 = ServiceUtils.getMapFor(outfile, column + 7); // layer 8 60-75 cm
Map<String, String> c75_90 = ServiceUtils.getMapFor(outfile, column + 8); // layer 9 75-90 cm
Map<String, String> c90_105 = ServiceUtils.getMapFor(outfile, column + 9); // layer 10 90-105 cm
if (LOG.isLoggable(Level.INFO)) {
LOG.info("vswc 0-2 : " + c0_2);
LOG.info("vswc 2-5 : " + c2_5);
}
// lisDates of harvest from schedule file
// List<String> harvestDates = getDates(LOG, starty, endy, schFile, croptype, termination);
// extract the values based on keys (harvest dates) into columnVals
List<String> columnVals = new ArrayList<>();
for (LocalDate date = starty; date.isBefore(endy); date = date.plusDays(7)) {
String tmp = date.format(DateTimeFormatter.ISO_ORDINAL_DATE);
String val0_2 = c0_2.get(tmp);
String val2_5 = c2_5.get(tmp);
String val5_10 = c5_10.get(tmp);
String val10_20 = c10_20.get(tmp);
String val20_30 = c20_30.get(tmp);
String val30_45 = c30_45.get(tmp);
String val45_60 = c45_60.get(tmp);
String val60_75 = c60_75.get(tmp);
String val75_90 = c75_90.get(tmp);
String val90_105 = c90_105.get(tmp);
if (val0_2 == null || val2_5 == null || val5_10 == null || val10_20 == null
|| val20_30 == null || val30_45 == null || val45_60 == null || val60_75 == null
|| val75_90 == null || val90_105 == null) {
throw new ServiceException("No value for date: " + date.format(DateTimeFormatter.ISO_DATE));
}
Double weightedAvg = (Double.parseDouble(val0_2) * 2
+ Double.parseDouble(val2_5) * 3
+ Double.parseDouble(val5_10) * 5
+ Double.parseDouble(val10_20) * 10
+ Double.parseDouble(val20_30) * 10
+ Double.parseDouble(val30_45) * 15
+ Double.parseDouble(val45_60) * 15
+ Double.parseDouble(val60_75) * 15
+ Double.parseDouble(val75_90) * 15
+ Double.parseDouble(val90_105) * 10) / 100; // 90-105 just 10 because we have data for 100cm tot
if (weightedAvg > 1.0) {
String msg = "Soil moisture bigger than 1";
throw new IllegalArgumentException(msg);
}
String val = String.valueOf(weightedAvg);
columnVals.add(val);
}
if (LOG.isLoggable(Level.INFO)) {
LOG.info("columnVals " + columnVals);
}
// // create the average of those values
// double avg = columnVals.stream().mapToDouble(Double::parseDouble).average().getAsDouble();
//
// if (LOG.isLoggable(Level.INFO)) {
// LOG.info("avg: " + avg);
// }
return columnVals.stream().mapToDouble(Double::parseDouble).toArray();
}
static double[] getSimulatedYearSummaryOUT(SessionLogger LOG, File outfile, String column,
int starty, int endy, Double nodata) throws IOException, ServiceException {
// get the raw values from lis file: as map
// e.g. time -> cgracc
Map<String, String> val = ServiceUtils.getMapFor(outfile, column);
if (LOG.isLoggable(Level.INFO)) {
LOG.info("N2O emissions : " + val);
}
// lisDates of harvest from schedule file
// List<String> harvestDates = getDates(LOG, starty, endy, schFile, croptype, termination);
// extract the values based on keys (harvest dates) into columnVals
List<String> columnVals = new ArrayList<>();
for (int i = starty + MODEL_OFFSET; i <= endy + MODEL_OFFSET; i++) {
String v = val.get(String.valueOf(i) + ".00");
if (v == null) {
throw new ServiceException("No value for year: " + i);
}
columnVals.add(String.valueOf(v));
}
if (LOG.isLoggable(Level.INFO)) {
LOG.info("columnVals " + columnVals);
}
// // create the average of those values
// double avg = columnVals.stream().mapToDouble(Double::parseDouble).average().getAsDouble();
//
// if (LOG.isLoggable(Level.INFO)) {
// LOG.info("avg: " + avg);
// }
return columnVals.stream().mapToDouble(Double::parseDouble).toArray();
}
static double[] getSimulatedValues(SessionLogger LOG, File schFile, File lisFile, String column,
int starty, int endy, String croptype, String termination, Double nodata) throws Exception {
int starty_list = starty + MODEL_OFFSET; // Truterra .sch
int endy_list = endy + MODEL_OFFSET; // Truterra .sch
List<Integer> cropYear = IntStream.rangeClosed(starty_list, endy_list).boxed().collect(Collectors.toList());
// get the raw values from lis file: as map
// e.g. time -> cgracc
Map<String, String> c = ServiceUtils.getMapFor(lisFile, column);
if (LOG.isLoggable(Level.INFO)) {
LOG.info("caggr : " + c);
}
// lisDates of harvest from schedule file
List<String> harvestDates = getDates(LOG, starty, endy, schFile, croptype, termination);
// extract the values based on keys (harvest dates) into columnVals
List<String> columnVals = new ArrayList<>();
for (Integer y : cropYear) {
// for (String harvestDate : harvestDates) {
String hy = harvestDatesHasYear(harvestDates, y);
if (!hy.isEmpty()) {
String caggr = c.get(hy);
if (caggr == null) {
throw new ServiceException("No caggr value for harvestDate: " + y);
}
columnVals.add(c.get(hy));
} else {
columnVals.add(nodata.toString());
}
}
if (LOG.isLoggable(Level.INFO)) {
LOG.info("columnVals " + columnVals);
}
// // create the average of those values
// double avg = columnVals.stream().mapToDouble(Double::parseDouble).average().getAsDouble();
//
// if (LOG.isLoggable(Level.INFO)) {
// LOG.info("avg: " + avg);
// }
return columnVals.stream().mapToDouble(Double::parseDouble).toArray();
}
private static String harvestDatesHasYear(List<String> harvestDates, Integer y) {
for (String date : harvestDates) {
String val = date.split("\\.")[0];
String mm = date.split("\\.")[1];
if (mm.contains("00")) {
if ((Integer.parseInt(val) - 1) == y) {
return date;
}
} else if (Integer.parseInt(val) == y) {
return date;
}
}
return "";
}
public static boolean isLeapYear(int year) {
Calendar cal = Calendar.getInstance();
cal.set(Calendar.YEAR, year);
return cal.getActualMaximum(Calendar.DAY_OF_YEAR) > 365;
}
static double getVal(SessionLogger LOG, File schFile, File lisFile, String column,
int year) throws Exception {
// get the raw values from lis file: as map
// e.g. time -> cgracc
Map<String, String> c = ServiceUtils.getMapFor(lisFile, column);
if (LOG.isLoggable(Level.INFO)) {
LOG.info("caggr : " + c);
}
String tdate;
if (isLeapYear(year)) {
tdate = String.valueOf(year) + ".366";
} else {
tdate = String.valueOf(year) + ".365";
}
String date = DateConversion.date2daycentLis(tdate);
// extract the values based on keys (harvest dates) into columnVals
String somsc = c.get(date);
if (somsc == null) {
throw new ServiceException("No somsc value for year: " + year);
}
if (LOG.isLoggable(Level.INFO)) {
LOG.info("somsc " + somsc);
}
return Double.parseDouble(somsc);
}
static List<String> getDates(SessionLogger LOG, int starty, int endy,
File schFile, String croptype, String termination) throws IOException {
List<String> schDates = ServiceUtils.getCropHarvest(schFile, croptype, termination);
if (LOG.isLoggable(Level.INFO)) {
LOG.info("schDates: " + schDates);
}
List<String> filtered_schDates = new ArrayList<>();
// filter by date range (starty - endy)
for (String schDate : schDates) {
String[] sd = schDate.split("\\.");
int y = Integer.parseInt(sd[0]);
if (y >= starty && y <= endy) {
if (termination.equals("LAST")) {
int day = Integer.parseInt(sd[1]) - 30; // one month earlier
schDate = y + "." + day;
}
filtered_schDates.add(schDate);
}
}
if (LOG.isLoggable(Level.INFO)) {
LOG.info("Filtered dates: " + filtered_schDates);
}
// convert all schDates to lisDates
List<String> lisDates = new ArrayList<>();
for (String schDate : filtered_schDates) {
lisDates.add(DateConversion.date2daycentLis(schDate));
}
if (LOG.isLoggable(Level.INFO)) {
LOG.info("lisDates: " + lisDates);
}
return lisDates;
}
// public static void main(String[] args) {
// Integer a = new Double("2077.00").intValue();
// System.out.println(a);
// }
public static void main(String[] args) throws Exception {
ObjFunc of = ObjFunc.of(ObjFunc.NS);
String path = "/tmp/csip/work/21/14/0a6c933f-b232-11ed-86f8-bd73f95f4079/";
// calcObjFunc(new SessionLogger(),
// new File("/tmp/csip/work/22/15/db0e4255-1be8-11ec-b04a-738330b2f29e/Truterra.sch"),
// new File("/tmp/csip/work/22/15/db0e4255-1be8-11ec-b04a-738330b2f29e/Truterra.lis"),
// "yield", "60, 2011, 2020, W4");
//
// calcObjFunc(new SessionLogger(),
// new File("/home/sidereus/documents/daycentsim/wheat/check/Truterra.sch"),
// new File("/home/sidereus/documents/daycentsim/wheat/check/Truterra.lis"),
// "yield", "180, 2011, 2020, C13");
// calcObjFunc(new SessionLogger(),
// new File("/tmp/csip/work/22/15/db0e4255-1be8-11ec-b04a-738330b2f29e/Truterra.sch"),
// new File("/tmp/csip/work/22/15/db0e4255-1be8-11ec-b04a-738330b2f29e/Truterra.lis"),
// "yield", "111.67, 2011, 2020, SORG3");
// calcObjFunc(of, new SessionLogger(),
// new File("/home/sidereus/Downloads/arr/tmp/Truterra.sch"),
// new File("/home/sidereus/Downloads/arr/tmp/Truterra.lis"),
// new File("/home/sidereus/Downloads/arr/tmp/vswc.out"),
// new File("/home/sidereus/Downloads/arr/tmp/year_summary.out"),
// "n2o", "[0.0301, 0.0301, 0.0282], 2013, 2015, n2o", -9999.0);
//
// calcObjFunc(new SessionLogger(),
// new File("/tmp/csip/work/09/12/16f716fa-e0e0-11eb-ad10-23d87c956bee/Truterra.sch"),
// new File("/tmp/csip/work/09/12/16f716fa-e0e0-11eb-ad10-23d87c956bee/Truterra.lis"),
// "biomass", "120, 2011, 2020, CC2");
calcObjFunc(of, new SessionLogger(),
new File(path + "Truterra.sch"),
new File(path + "Truterra.lis"),
new File(path + "vswc.out"),
new File(path + "year_summary.out"),
"n2o", "[2.073252116447484, 2.073252116447484, 2.073252116447484], 2018, 2020, n2o", -9999.0);
// calcObjFunc(of, new SessionLogger(),
// new File("/home/sidereus/Downloads/archive/Truterra.sch"),
// new File("/home/sidereus/Downloads/archive/Truterra.lis"),
// new File("/home/sidereus/Downloads/archive/vswc.out"),
// "vswc", "[0.3354247957468033, 0.3432268388569355, 0.34121252596378326, 0.3451493978500366, 0.33685942739248276], 2015-04-01, 2015-04-30, vswc", -9999.0);
}
static double[] parseObsDouble(String obsValStr) {
String[] vals = obsValStr.split("\\s*,\\s*");
return Arrays.stream(vals).mapToDouble(Double::parseDouble).toArray();
}
static double calcObjFunc(ObjFunc objfunc, SessionLogger LOG, File schFile, File lisFile, File vswc, File n2o,
String target, String targetInfo, Double nodata) throws Exception {
// objfunc is ot used yet
if (target.equals("yield")) {
String[] ti = targetInfo.split("\\s*]\\s*");
if (ti.length != 2) {
throw new ServiceException("Invalid targetinfo for yield.");
}
String obsValStr = ti[0].replaceAll("\\[", ""); // obs data value for period
String[] vals = ti[1].split("\\s*,\\s*");
if (vals.length != 4) {
throw new ServiceException("Invalid targetinfo for yeild crop and years.");
}
String start = vals[1]; // start
String end = vals[2]; // end
String ct = vals[3]; // croptype (e.g. C5)
if (LOG.isLoggable(Level.INFO)) {
LOG.info(" objfunc info: " + Arrays.toString(ti));
}
double[] obsVal = parseObsDouble(obsValStr);
// simulated yield
double[] simVal = getSimulatedValues(LOG, schFile, lisFile,
"cgracc", Integer.parseInt(start), Integer.parseInt(end), ct, "HARV", nodata);
if (obsVal.length != simVal.length) {
String msg = "Variable " + ct + " length of observed " + obsVal.length + " differs from length of simulated " + simVal.length;
throw new IllegalArgumentException(msg);
}
Double conv = yieldConv.get(ct);
if (conv == null) {
throw new ServiceException("No yield conversion factor for: " + ct);
}
simVal = DoubleStream.of(simVal).map(v -> (v != nodata) ? v * conv : v).toArray();
if (LOG.isLoggable(Level.INFO)) {
LOG.info("sim yield: " + Arrays.toString(simVal));
}
List<Double> vSim = Arrays.stream(simVal).boxed().collect(Collectors.toList());
List<Double> vObs = Arrays.stream(obsVal).boxed().collect(Collectors.toList());
List<Integer> index = new ArrayList<>();
for (int i = 0; i < vSim.size(); i++) {
if (vSim.get(i).equals(nodata)) {
index.add(i);
}
}
if (index.size() >= vSim.size()) {
String msg = vSim.size() + " simulated values vs " + index.size() + " values to remove variable: " + ct;
throw new IllegalArgumentException(msg);
}
if (index.size() >= vObs.size()) {
String msg = vObs.size() + " observed values vs " + index.size() + " values to remove variable: " + ct;
throw new IllegalArgumentException(msg);
}
Collections.reverse(index);
for (int v : index) {
vSim.remove(v);
vObs.remove(v);
}
if (vSim.isEmpty()) {
String msg = "Simulated " + ct + " is empty";
throw new NullPointerException(msg);
}
if (vObs.isEmpty()) {
String msg = "Observed " + ct + " is empty";
throw new NullPointerException(msg);
}
if (vSim.size() != vObs.size()) {
String msg = "Simulated and observed have different size for variable " + ct;
throw new IllegalArgumentException(msg);
}
simVal = vSim.stream().mapToDouble(Double::doubleValue).toArray();
obsVal = vObs.stream().mapToDouble(Double::doubleValue).toArray();
return objfunc.eval(obsVal, simVal, nodata); // double check the NA
} else if (target.equals("biomass")) {
String[] ti = targetInfo.split("\\s*]\\s*");
if (ti.length != 2) {
throw new ServiceException("Invalid targetinfo for biomass.");
}
String obsValStr = ti[0].replaceAll("\\[", ""); // obs data value for period
String[] vals = ti[1].split("\\s*,\\s*");
if (vals.length != 4) {
throw new ServiceException("Invalid targetinfo for biomass crop and years.");
}
String start = vals[1]; // start
String end = vals[2]; // end
String ct = vals[3]; // croptype (e.g. C5)
if (LOG.isLoggable(Level.INFO)) {
LOG.info(" objfunc info: " + Arrays.toString(ti));
}
double[] obsVal = parseObsDouble(obsValStr);
// simulated yield
double[] simVal = getSimulatedValues(LOG, schFile, lisFile,
"crmvst", Integer.parseInt(start), Integer.parseInt(end), ct, "HARV", nodata);
if (obsVal.length != simVal.length) {
String msg = "Variable " + ct + " length of observed " + obsVal.length + " differs from length of simulated " + simVal.length;
throw new IllegalArgumentException(msg);
}
Double conv = yieldConv.get(ct);
if (conv == null) {
throw new ServiceException("No biomass conversion factor for: " + ct);
}
simVal = DoubleStream.of(simVal).map(v -> (v != nodata) ? v * conv : v).toArray();
if (LOG.isLoggable(Level.INFO)) {
LOG.info("sim biomass: " + Arrays.toString(simVal));
}
List<Double> vSim = Arrays.stream(simVal).boxed().collect(Collectors.toList());
List<Double> vObs = Arrays.stream(obsVal).boxed().collect(Collectors.toList());
List<Integer> index = new ArrayList<>();
for (int i = 0; i < vSim.size(); i++) {
if (vSim.get(i).equals(nodata)) {
index.add(i);
}
}
if (index.size() >= vSim.size()) {
String msg = vSim.size() + " simulated values vs " + index.size() + " values to remove variable: " + ct;
throw new IllegalArgumentException(msg);
}
if (index.size() >= vObs.size()) {
String msg = vObs.size() + " observed values vs " + index.size() + " values to remove variable: " + ct;
throw new IllegalArgumentException(msg);
}
Collections.reverse(index);
for (int v : index) {
vSim.remove(v);
vObs.remove(v);
}
if (vSim.isEmpty()) {
String msg = "Simulated " + ct + " is empty";
throw new NullPointerException(msg);
}
if (vObs.isEmpty()) {
String msg = "Observed " + ct + " is empty";
throw new NullPointerException(msg);
}
if (vSim.size() != vObs.size()) {
String msg = "Simulated and observed have different size for variable " + ct;
throw new IllegalArgumentException(msg);
}
simVal = vSim.stream().mapToDouble(Double::doubleValue).toArray();
obsVal = vObs.stream().mapToDouble(Double::doubleValue).toArray();
return objfunc.eval(obsVal, simVal, nodata); // double check the NA
} else if (target.equals("root")) {
String[] ti = targetInfo.split("\\s*]\\s*");
if (ti.length != 2) {
throw new ServiceException("Invalid targetinfo for root.");
}
String obsValStr = ti[0].replaceAll("\\[", ""); // obs data value for period
String[] vals = ti[1].split("\\s*,\\s*");
if (vals.length != 4) {
throw new ServiceException("Invalid targetinfo for root crop and years.");
}
String start = vals[1]; // start
String end = vals[2]; // end
String ct = vals[3]; // croptype (e.g. C5)
if (LOG.isLoggable(Level.INFO)) {
LOG.info(" objfunc info: " + Arrays.toString(ti));
}
double[] obsVal = parseObsDouble(obsValStr);
// simulated yield
double[] simVal = getSimulatedValues(LOG, schFile, lisFile,
"bgcmacc", Integer.parseInt(start), Integer.parseInt(end), ct, "HARV", nodata);
if (obsVal.length != simVal.length) {
String msg = "Variable " + ct + " length of observed " + obsVal.length + " differs from length of simulated " + simVal.length;
throw new IllegalArgumentException(msg);
}
Double conv = yieldConv.get(ct);
if (conv == null) {
throw new ServiceException("No root conversion factor for: " + ct);
}
simVal = DoubleStream.of(simVal).map(v -> (v != nodata) ? v * conv : v).toArray();
if (LOG.isLoggable(Level.INFO)) {
LOG.info("sim root: " + Arrays.toString(simVal));
}
List<Double> vSim = Arrays.stream(simVal).boxed().collect(Collectors.toList());
List<Double> vObs = Arrays.stream(obsVal).boxed().collect(Collectors.toList());
List<Integer> index = new ArrayList<>();
for (int i = 0; i < vSim.size(); i++) {
if (vSim.get(i).equals(nodata)) {
index.add(i);
}
}
if (index.size() >= vSim.size()) {
String msg = vSim.size() + " simulated values vs " + index.size() + " values to remove variable: " + ct;
throw new IllegalArgumentException(msg);
}
if (index.size() >= vObs.size()) {
String msg = vObs.size() + " observed values vs " + index.size() + " values to remove variable: " + ct;
throw new IllegalArgumentException(msg);
}
Collections.reverse(index);
for (int v : index) {
vSim.remove(v);
vObs.remove(v);
}
if (vSim.isEmpty()) {
String msg = "Simulated " + ct + " is empty";
throw new NullPointerException(msg);
}
if (vObs.isEmpty()) {
String msg = "Observed " + ct + " is empty";
throw new NullPointerException(msg);
}
if (vSim.size() != vObs.size()) {
String msg = "Simulated and observed have different size for variable " + ct;
throw new IllegalArgumentException(msg);
}
simVal = vSim.stream().mapToDouble(Double::doubleValue).toArray();
obsVal = vObs.stream().mapToDouble(Double::doubleValue).toArray();
return objfunc.eval(obsVal, simVal, nodata); // double check the NA
} else if (target.equals("soc")) {
String[] ti = targetInfo.split("\\s*,\\s*");
if (ti.length != 2) {
throw new ServiceException("Invalid targetinfo for yield.");
}
String obsValStr = ti[0]; // obs data value for period
String year = ti[1]; // year
if (LOG.isLoggable(Level.INFO)) {
LOG.info(" objfunc info: " + Arrays.toString(ti));
}
double simVal = getVal(LOG, schFile, lisFile,
"somsc", Integer.parseInt(year));
double obsVal = Double.parseDouble(obsValStr);
double[] obsArr = new double[]{obsVal};
double[] simArr = new double[]{simVal};
double v = Math.abs(obsVal - simVal);
if (LOG.isLoggable(Level.INFO)) {
LOG.info(" efficiency: " + v);
}
return v;
} else if (target.equals("vswc")) {
String[] ti = targetInfo.split("\\s*]\\s*");
if (ti.length != 2) {
throw new ServiceException("Invalid targetinfo for volumetric soil water content.");
}
String obsValStr = ti[0].replaceAll("\\[", ""); // obs data value for period
String[] vals = ti[1].split("\\s*,\\s*");
if (vals.length != 4) {
throw new ServiceException("Invalid targetinfo for volumetric soil water content and years.");
}
LocalDate start = LocalDate.parse(vals[1]); // start format YYYY-MM-DD
LocalDate end = LocalDate.parse(vals[2]); // end format YYYY-MM-DD
String ct = vals[3]; // croptype (e.g. C5)
if (LOG.isLoggable(Level.INFO)) {
LOG.info(" objfunc info: " + Arrays.toString(ti));
}
double[] obsVal = parseObsDouble(obsValStr);
int column = 2;
// simulated yield
double[] simVal = getSimulatedOUT(LOG, vswc, column, start, end, nodata);
if (LOG.isLoggable(Level.INFO)) {
LOG.info("sim yield: " + Arrays.toString(simVal));
}
List<Double> vSim = Arrays.stream(simVal).boxed().collect(Collectors.toList());
List<Double> vObs = Arrays.stream(obsVal).boxed().collect(Collectors.toList());
List<Integer> index = new ArrayList<>();
for (int i = 0; i < vSim.size(); i++) {
if (vSim.get(i).equals(nodata)) {
index.add(i);
}
}
Collections.reverse(index);
for (int v : index) {
vSim.remove(v);
vObs.remove(v);
}
if (vSim.isEmpty()) {
String msg = "Simulated " + ct + " is empty";
throw new NullPointerException(msg);
}
if (vObs.isEmpty()) {
String msg = "Observed " + ct + " is empty";
throw new NullPointerException(msg);
}
if (vSim.size() != vObs.size()) {
String msg = "Simulated and observed have different size for variable " + ct;
throw new IllegalArgumentException(msg);
}
simVal = vSim.stream().mapToDouble(Double::doubleValue).toArray();
obsVal = vObs.stream().mapToDouble(Double::doubleValue).toArray();
return objfunc.eval(obsVal, simVal, -9999.0); // double check the NA
} else if (target.equals("n2o")) {
String[] ti = targetInfo.split("\\s*]\\s*");
if (ti.length != 2) {
throw new ServiceException("Invalid targetinfo for N2O emissions.");
}
String obsValStr = ti[0].replaceAll("\\[", ""); // obs data value for period
String[] vals = ti[1].split("\\s*,\\s*");
if (vals.length != 4) {
throw new ServiceException("Invalid targetinfo for N2O emissions and years.");
}
int start = Integer.parseInt(vals[1]);
int end = Integer.parseInt(vals[2]);
String ct = vals[3]; // croptype (e.g. C5)
if (LOG.isLoggable(Level.INFO)) {
LOG.info(" objfunc info: " + Arrays.toString(ti));
}
double[] obsVal = parseObsDouble(obsValStr);
String column = "N2Oflux";
// simulated yield
double[] simVal = getSimulatedYearSummaryOUT(LOG, n2o, column, start, end, nodata);
if (LOG.isLoggable(Level.INFO)) {
LOG.info("sim yield: " + Arrays.toString(simVal));
}
List<Double> vSim = Arrays.stream(simVal).boxed().collect(Collectors.toList());
List<Double> vObs = Arrays.stream(obsVal).boxed().collect(Collectors.toList());
List<Integer> index = new ArrayList<>();
for (int i = 0; i < vSim.size(); i++) {
if (vSim.get(i).equals(nodata)) {
index.add(i);
}
}
Collections.reverse(index);
for (int v : index) {
vSim.remove(v);
vObs.remove(v);
}
if (vSim.isEmpty()) {
String msg = "Simulated " + ct + " is empty";
throw new NullPointerException(msg);
}
if (vObs.isEmpty()) {
String msg = "Observed " + ct + " is empty";
throw new NullPointerException(msg);
}
if (vSim.size() != vObs.size()) {
String msg = "Simulated and observed have different size for variable " + ct;
throw new IllegalArgumentException(msg);
}
simVal = vSim.stream().mapToDouble(Double::doubleValue).toArray();
obsVal = vObs.stream().mapToDouble(Double::doubleValue).toArray();
return objfunc.eval(obsVal, simVal, -9999.0); // double check the NA
} else {
throw new Exception("calibration target not supported: " + target);
}
}
// static final Map<String, ObjectiveFunction> OF = new HashMap<>();
// static {
// OF.put("kge", new KGE());
// OF.put("ns", new NS());
// OF.put("nslog", new NS2LOG());
// OF.put("nslog1p", new NSLOG1P());
// OF.put("nslog2", new NSLOG2());
// OF.put("rmse", new RMSE());
// OF.put("trmse", new TRMSE());
// OF.put("pbias", new PBIAS());
// }
//
// private List<String> getRequestedObjfunc() {
// List<String> l = new ArrayList<>();
// for (String p : parameter().getNames()) {
// if (p.toLowerCase().startsWith("pbias.")) {
// l.add(p);
// }
// }
// return l;
// }
/////////////////////
protected Map<String, List<String>> getHarvValues(SessionLogger LOG, String harvFile, String column,
int starty, int endy) throws Exception {
int starty_list = starty + MODEL_OFFSET; // Truterra .sch
int endy_list = endy + MODEL_OFFSET; // Truterra .sch
List<Integer> cropYear = IntStream.rangeClosed(starty_list, endy_list).boxed().collect(Collectors.toList());
// get the raw values from lis file: as map
// e.g. time -> cgracc
Map<String, List<String>> c = ServiceUtils.getMapList(workspace().getFile(harvFile), column);
return c;
}
protected void parseLis(Map<Integer, Double> N2Oflux, Map<Integer, Double> CH4flux) throws FileNotFoundException, JSONException, Exception {
List<Integer> practiceChange = new LinkedList<>();
// adjusted to get
for (int i = staticYearPractChange; i <= projectionYear; i++) {
practiceChange.add(i);
}
String lisFile = schedule + ".lis";
String schFile = schedule + ".sch";
String harvFile = "harvest.csv";
Map<String, List<String>> harvVals = getHarvValues(LOG, harvFile, "crmvst", staticYearPractChange, projectionYear);
Map<String, List<String>> cgraccVals = getHarvValues(LOG, harvFile, "cgrain", staticYearPractChange, projectionYear);
int lineNumber = 1;
int colTime = 0;
boolean skiplastline = Boolean.FALSE;
try (Scanner scanner = new Scanner(workspace().getFile(lisFile));) {
String[] prevData = null;
Integer yearNewMgt = practiceChange.remove(0); // first element always
while (scanner.hasNextLine()) {
String line = scanner.nextLine();
double prevCgain = 0;
if (lineNumber == 1) {
// read header
String[] data = line.split("\\s+");
for (int col = 0; col < data.length; col++) {
if (data[col].equals("cgracc")) {
colGracc = col;
} else if (data[col].equals("agcacc")) {
colAbove = col;
} else if (data[col].equals("bgcjacc")) {
colBelowFineRoots = col;
} else if (data[col].equals("bgcmacc")) {
colBelowMatureRoots = col;
} else if (data[col].equals("somsc")) {
colSOM = col;
} else if (data[col].equals("time")) {
colTime = col;
}
}
} else if (lineNumber == 2) {
// skip line because empty
} else {
// check the line
String[] data = line.split("\\s+");
double year = Double.parseDouble(data[colTime]);
if (prevData == null && year == (yearNewMgt + MODEL_OFFSET)) {
prevData = data;
}
if (!skiplastline) {
// +2000 because 4000 years of simulation
// +1 because of extra year - December 2012 = 2013.00 from Daycent .lis file
if (year == (yearNewMgt + MODEL_OFFSET + 1)) {
String sYear = String.valueOf(yearNewMgt + MODEL_OFFSET) + ".00";
List<Double> s = null;
List<Double> cgr = null;
if (harvVals.containsKey(sYear)) {
s = harvVals.get(sYear).stream().map(Double::valueOf).collect(Collectors.toList());
} else {
s = new ArrayList<>();
s.add(0.0);
}
if (cgraccVals.containsKey(sYear)) {
cgr = cgraccVals.get(sYear).stream().map(Double::valueOf).collect(Collectors.toList());
} else {
cgr = new ArrayList<>();
cgr.add(0.0);
}
double som = Double.parseDouble(prevData[colSOM]);
prevCgain = som * 0.00404686 * area;
Integer actYear = yearNewMgt;
results().put(actYear.toString(), getValues(data, prevCgain, N2Oflux.get(actYear), CH4flux.get(actYear), s, cgr));
prevData = data;
// last year is duplicated and need to skip it
if (!practiceChange.isEmpty()) {
yearNewMgt = practiceChange.remove(0);
} else {
skiplastline = Boolean.TRUE;
}
}
}
}
lineNumber++;
}
}
}
private JSONArray getValues(String[] data, double prevCgain, double comp_n2o_emission, double comp_ch4_emission, List<Double> biomass, List<Double> cgracc) throws JSONException {
// double comp_crop_yld_c = Double.parseDouble(data[colGracc]) * 0.00404686 * area;
List<Double> comp_crop_yld_c = new ArrayList<>();
for (Double v : cgracc) {
double tmp = v * 0.00404686 * area;
comp_crop_yld_c.add(tmp);
}
List<Double> comp_crop_biom_c = new ArrayList<>();
for (Double v : biomass) {
double tmp = v * 0.00404686 * area;
comp_crop_biom_c.add(tmp);
}
double comp_crop_res_c = (Double.parseDouble(data[colAbove])
+ Double.parseDouble(data[colBelowFineRoots])
+ Double.parseDouble(data[colBelowMatureRoots])) * 0.00404686 * area;
double comp_soil_c_stock = Double.parseDouble(data[colSOM]) * 0.00404686 * area;
double comp_soil_c_stock_unit_area = Double.parseDouble(data[colSOM]);
double comp_soil_c_gain = comp_soil_c_stock - prevCgain;
comp_n2o_emission = comp_n2o_emission * 1.895087; // g/m2 of N2O-N to Mg/ac CO2e
comp_n2o_emission = comp_n2o_emission * area; // Mg/ac CO2e to Mg (metric tons) CO2e
comp_ch4_emission = comp_ch4_emission * 0.453248; // g/m2 of CH4-C to Mg/ac CO2e
comp_ch4_emission = comp_ch4_emission * area; // Mg/ac CO2e to Mg (metric tons) CO2e
JSONObject jy = new JSONObject()
.put("name", "comp_crop_yld_c")
.put("description", "Crop yield carbon of intersected mapunit soil component leaving field")
.put("units", "Metric tons")
.put("value", comp_crop_yld_c);
JSONObject jb = new JSONObject()
.put("name", "comp_crop_biom_c")
.put("description", "Crop biomass carbon of intersected mapunit soil component leaving field")
.put("units", "Metric tons")
.put("value", comp_crop_biom_c);
JSONObject jc = new JSONObject()
.put("name", "comp_crop_res_c")
.put("description", "Crop residue carbon above and below ground of intersected mapunit soil component remaining in field")
.put("units", "Metric tons")
.put("value", comp_crop_res_c);
JSONObject js = new JSONObject()
.put("name", "comp_soil_c_stock")
.put("description", "Soil carbon stock of intersected mapunit soil component at the end of crop")
.put("units", "Metric tons")
.put("value", comp_soil_c_stock);
JSONObject jg = new JSONObject()
.put("name", "comp_soil_c_gain")
.put("description", "Soil carbon stock gain or loss for intersected mapunit soil component through crop year")
.put("units", "Metric tons")
.put("value", comp_soil_c_gain);
JSONObject jsua = new JSONObject()
.put("name", "comp_soil_c_stock_unit_area")
.put("description", "Soil carbon stock per unit area of intersected mapunit soil component at the end of crop")
.put("units", "g per meter squared")
.put("value", comp_soil_c_stock_unit_area);
JSONObject n2o_emission = new JSONObject()
.put("name", "comp_n2o_emission")
.put("description", "Nitrous oxide emissions from farm field in carbon dioxide (CO2) equivalents")
.put("units", "Metric tons")
.put("value", comp_n2o_emission);
JSONObject ch4_emission = new JSONObject()
.put("name", "comp_ch4_emission")
.put("description", "Methane emissions from farm field in carbon dioxide (CO2) equivalents")
.put("units", "Metric tons")
.put("value", comp_ch4_emission);
// JSONObject net_co2_removed = new JSONObject()
// .put("name", "comp_net_co2_removed_unit_area")
// .put("description", "Soil carbon CO2 equivalents minus CO2 equivalents for nitrous oxide and methans")
// .put("units", "Metric tons")
// .put("value", "");
JSONArray ja = new JSONArray()
.put(jy)
.put(jb)
.put(jc)
.put(js)
.put(jg)
.put(jsua)
.put(n2o_emission)
.put(ch4_emission);
return ja;
}
public void checkHarvest() throws FileNotFoundException {
String filename = schedule + ".lis";
int lineNumber = 1;
int colGracc = 0;
int colTime = 0;
try (Scanner scanner = new Scanner(workspace().getFile(filename));) {
while (scanner.hasNextLine()) {
String line = scanner.nextLine();
if (lineNumber == 1) {
// read header
String[] data = line.split("\\s+");
for (int col = 0; col < data.length; col++) {
if (data[col].equals("cgracc")) {
colGracc = col;
} else if (data[col].equals("time")) {
colTime = col;
}
}
} else if (lineNumber == 2) {
// skip line because empty
} else {
// check the line
String[] data = line.split("\\s+");
double year = Double.parseDouble(data[colTime]);
if (year > 4010 && year < 4021) {
double grainHarvest = Double.parseDouble(data[colGracc]);
if (grainHarvest == 0.0) {
String msg = "cgracc for year " + year + " is " + grainHarvest;
throw new UnsupportedOperationException(msg);
}
}
}
lineNumber++;
}
}
}
static final Map<String, Map<String, String>> defMap = new HashMap() {
{
put("prdx", prdxDef);
put("ppdf1", ppdf1Def);
put("himax", himaxDef);
put("hiwsf", hiwsfDef);
put("ppdf2", ppdf2Def);
put("ppdf3", ppdf3Def);
put("ppdf4", ppdf4Def);
put("wscoeff1", wscoeff1Def);
put("wscoeff2", wscoeff2Def);
put("pramn", pramnDef);
put("pramx", pramxDef);
put("sfavail", sfavailDef);
}
};
static final Map<String, Map<String, String>> defTreeMap = new HashMap() {
{
put("prdx", prdxTree);
put("ppdf1", ppdf1Tree);
put("ppdf2", ppdf2Tree);
}
};
protected void countLayers() {
try {
profileDepths = new LinkedList<>();
List<Double> profiles = Files.lines(workspace().getFile("soils.in").toPath())
.map(str -> str.split("\\s+"))
.map(str -> Double.parseDouble(str[1]))
.collect(Collectors.toList());
double[] defaultProfile = new double[]{10, 20, 15, 15, 30, 30, 30, 30, 30, 30};
double val = 0;
double bottom = profiles.get(profiles.size() - 1);
for (int i = 0; i < defaultProfile.length; i++) {
double prof = defaultProfile[i];
val += prof;
if (val == bottom) {
profileDepths.add(prof);
break;
} else if (val > bottom) {
double tmpval = val - prof;
profileDepths.add(bottom - tmpval);
break;
} else {
profileDepths.add(prof);
}
}
nlayer = profileDepths.size(); // - 2; // the first three layers are meshed into 1
} catch (IOException ex) {
throw new RuntimeException(ex.getMessage());
}
}
protected Map<String, Map<String, Double>> dictPopulation(Map<String, Map<String, Double>> hashmap, String s) throws ServiceException {
String[] parts = s.split("\\.");
String cropName = parts[1];
String parameterName = parts[2];
Double parameterValue = parameter().getDouble(s);
if (hashmap.containsKey(cropName)) {
hashmap.get(cropName).put(parameterName, parameterValue);
} else {
Map<String, Double> val1 = new HashMap<>();
val1.put(parameterName, parameterValue);
hashmap.put(cropName, val1);
}
return hashmap;
}
protected void fillCropValues() {
for (Map.Entry<String, Map<String, Double>> entry : crops.entrySet()) {
List<String> cropparamList = Arrays.asList("prdx", "ppdf1", "ppdf2", "ppdf3", "ppdf4", "wscoeff1", "wscoeff2", "himax", "hiwsf", "pramn", "pramx", "sfavail");
for (String param : cropparamList) {
if (!entry.getValue().containsKey(param)) {
crops.get(entry.getKey()).put(param, Double.parseDouble(defMap.get(param).get(entry.getKey())));
}
}
}
}
protected void fillTreeValues() {
for (Map.Entry<String, Map<String, Double>> entry : trees.entrySet()) {
List<String> treeparamList = Arrays.asList("prdx", "ppdf1", "ppdf2");
for (String param : treeparamList) {
if (!entry.getValue().containsKey(param)) {
trees.get(entry.getKey()).put(param, Double.parseDouble(defTreeMap.get(param).get(entry.getKey())));
}
}
}
}
protected void fillFileValues(List<String> paramList, Map<String, Map<String, Double>> hashmap, Map<String, String> defName) {
for (Map.Entry<String, Map<String, Double>> entry : hashmap.entrySet()) {
for (String param : paramList) {
if (!entry.getValue().containsKey(param)) {
hashmap.get(entry.getKey()).put(param, Double.parseDouble(defName.get(param)));
}
}
}
}
protected void fillFileFixes(List<String> paramList, Map<String, Map<String, Double>> hashmap, Map<String, String> defName) {
for (Map.Entry<String, Map<String, Double>> entry : hashmap.entrySet()) {
for (String param : paramList) {
if (!entry.getValue().containsKey(param)) {
if (param == null) {
String msg = "Null " + paramList;
throw new NullPointerException(msg);
}
hashmap.get(entry.getKey()).put(param, Double.parseDouble(defName.get(param)));
}
}
}
}
protected void getJSONParams() throws JSONException, ServiceException {
List<String> paramList = Arrays.asList(
"fwloss1", "fwloss2", "fwloss3", "fwloss4",
"ag_fwloss1", "ag_fwloss2", "ag_fwloss3", "ag_fwloss4",
"pa_fwloss1", "pa_fwloss2", "pa_fwloss3", "pa_fwloss4",
"tt_fwloss1", "tt_fwloss2", "tt_fwloss3", "tt_fwloss4",
"ag_dec32", "pa_dec32", "ag_dec4", "pa_dec4", "pa_dec52", "ag_dec52",
"dec32", "dec4", "dec52",
"tt_dec32", "tt_dec4", "tt_dec52",
"ag_teff1", "ag_teff2", "ag_teff3", "ag_teff4",
"pa_teff1", "pa_teff2", "pa_teff3", "pa_teff4",
"tt_teff1", "tt_teff2", "tt_teff3", "tt_teff4",
"ps1s31", "ps1s32", "ps2s31", "ps2s32", "fleach3",
"pa_ps1s31", "pa_ps1s32", "pa_ps2s31", "pa_ps2s32",
"ag_ps1s31", "ag_ps1s32", "ag_ps2s31", "ag_ps2s32",
"tt_ps1s31", "tt_ps1s32", "tt_ps2s31", "tt_ps2s32",
"dec11", "dec12", "dec22", "dec21", "dec31", "dec51", "ag_fleach3", "pa_fleach3", "tt_fleach3",
"pmco22", "p2co22", "ps1co22", "p1co2a2", "p1co2b2", "p3co2",
"ag_pmco22", "ag_p2co22", "ag_ps1co22", "ag_p1co2a2", "ag_p1co2b2", "ag_p3co2",
"tt_pmco22", "tt_p2co22", "tt_ps1co22", "tt_p1co2a2", "tt_p1co2b2", "tt_p3co2",
"pa_pmco22", "pa_p2co22", "pa_ps1co22", "pa_p1co2a2", "pa_p1co2b2", "pa_p3co2",
"pa_dec11", "ag_dec11", "pa_dec12", "ag_dec12", "pa_dec21", "ag_dec21", "pa_dec22", "ag_dec22", "pa_dec31", "ag_dec31", "pa_dec51", "ag_dec51",
"tt_dec21", "tt_dec22", "tt_dec31", "tt_dec51", "tt_dec11", "tt_dec12");
List<String> siteparList = Arrays.asList("dmpflux", "pa_dmpflux", "ag_dmpflux", "tt_dmpflux",
"MaxNitAmt", "pa_MaxNitAmt", "ag_MaxNitAmt", "tt_MaxNitAmt",
"wfpsdnitadj", "pa_wfpsdnitadj", "ag_wfpsdnitadj", "tt_wfpsdnitadj",
"n2n2oadj", "pa_n2n2oadj", "ag_n2n2oadj", "tt_n2n2oadj");
List<String> lrrmList = Arrays.asList("basef");
List<String> soilList = Arrays.asList("fieldCapacity1", "fieldCapacity2",
"fieldCapacity3", "fieldCapacity4", "fieldCapacity5", "fieldCapacity6",
"fieldCapacity7", "fieldCapacity8", "fieldCapacity9", "fieldCapacity10",
"wiltingPoint1", "wiltingPoint2", "wiltingPoint3", "wiltingPoint4",
"wiltingPoint5", "wiltingPoint6", "wiltingPoint7", "wiltingPoint8",
"wiltingPoint9", "wiltingPoint10"
);
for (String s : JSONparams) {
String[] parts = s.split("\\.");
if (parts.length > 1) {
String cropType = parts[0];
String fileName = parts[1];
if (cropType.equals("crop")) {
crops = dictPopulation(crops, s);
} else if (cropType.equals("tree")) {
trees = dictPopulation(trees, s);
} else if (cropType.equals("param") && fileName.equals("fixes")) {
fixes = dictPopulation(fixes, s);
} else if (cropType.equals("param") && fileName.equals("lrrm")) {
lrrm = dictPopulation(lrrm, s);
} else if (cropType.equals("param") && fileName.equals("site")) {
sitepars = dictPopulation(sitepars, s);
} else if (cropType.equals("param") && fileName.equals("soil")) {
calibonly = Boolean.TRUE; // inject calibrated parameters into soil file
soilpars = dictPopulation(soilpars, s);
}
}
}
fillFileFixes(paramList, fixes, fixDef);
fillFileValues(lrrmList, lrrm, lrrmDef);
fillFileValues(siteparList, sitepars, siteparDef);
fillFileValues(soilList, soilpars, soilDef);
fillCropValues();
fillTreeValues();
}
protected void fetchSoil(Boolean calibonly, Integer counter) throws Exception {
ModelDataServiceCall mds = new ModelDataServiceCall()
.put(STREAM_FILE, fileAsJSON)
.put("cokey", cokey)
.put("calibration", calibonly)
.put("ignore_bad_caco3", Boolean.TRUE)
.put(soils.AoA.AOA_GEOMETRY, new JSONObject()
.put(TYPE, aoa_geometry.get(TYPE))
.put(COORDINATES, aoa_geometry.get(COORDINATES)))
.url(Config.getString("ghg.soilfile.url",
request().getCodebase() + "d/insoilfile/2.2"))
.withRetries(10) // 10 retries for soil as well
.withRetryPause(1000)
.call();
if (mds.serviceFinished()) {
mds.download("soils.in", workspace().getFile("soils.in"));
} else if (counter != null && counter >= 10) {
throw new RuntimeException("GHG Soil service error: " + mds.getError());
} else {
if (counter == null) {
counter = 1;
} else {
counter++;
}
LOG.info("Soil service Counter: " + counter);
fetchSoil(calibonly, counter);
}
}
}