From 853c45be493f78676ae0dc895fe11c97fc7eba23 Mon Sep 17 00:00:00 2001
From: bclayton-usgs <bclayton@usgs.gov>
Date: Wed, 26 Feb 2020 12:23:23 -0700
Subject: [PATCH] add initial Java file
---
.../nshmp/netcdf/NshmpNetcdfReader.java | 966 ++++++++++++++++++
src/main/resources/eclipse.importorder | 5 -
src/main/resources/nshmp.eclipse-format.xml | 916 -----------------
3 files changed, 966 insertions(+), 921 deletions(-)
create mode 100644 src/main/java/gov/usgs/earthquake/nshmp/netcdf/NshmpNetcdfReader.java
delete mode 100644 src/main/resources/eclipse.importorder
delete mode 100644 src/main/resources/nshmp.eclipse-format.xml
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/netcdf/NshmpNetcdfReader.java b/src/main/java/gov/usgs/earthquake/nshmp/netcdf/NshmpNetcdfReader.java
new file mode 100644
index 0000000..583492a
--- /dev/null
+++ b/src/main/java/gov/usgs/earthquake/nshmp/netcdf/NshmpNetcdfReader.java
@@ -0,0 +1,966 @@
+package gov.usgs.earthquake.nshmp.netcdf;
+
+import static com.google.common.base.Preconditions.checkArgument;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.EnumMap;
+import java.util.List;
+import java.util.Map;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+import java.util.stream.Collectors;
+
+import ucar.ma2.Array;
+import ucar.ma2.DataType;
+import ucar.ma2.InvalidRangeException;
+import ucar.nc2.Group;
+import ucar.nc2.Variable;
+import ucar.nc2.dataset.NetcdfDataset;
+
+import com.google.common.collect.Maps;
+import com.google.common.math.DoubleMath;
+
+import gov.usgs.earthquake.nshmp.data.XySequence;
+import gov.usgs.earthquake.nshmp.geo.Location;
+import gov.usgs.earthquake.nshmp.gmm.Imt;
+
+/**
+ *
+ * Interface to static hazard curves stored in netCDF
+ *
+ * This class is currently specific to NSHMP 2018a data release.
+ *
+ * TODO: generalize for any NSHMP model data release with subclasses per data
+ * release.
+ *
+ * TODO: Replace loops with streams
+ *
+ * TODO: Utilize XySequence.copyOf()
+ *
+ * TODO: Update netCDF file format, rename variables, implement enums,
+ * standardize attributes, remove Vs30 dimension from Imls
+ *
+ * @author U.S. Geological Survey
+ */
+public class NshmpNetcdfReader {
+
+ final String nshmpNetcdfFilename; // path to netCDF file
+ final String nshmpBaseGroup; // netCDF group path to model data
+
+ final NshmpNetcdfCoordinates nshmpCoords;
+
+ private Logger logger;
+
+ /**
+ * @param nshmpNetcdfFilename
+ * @param nshmpBaseGroup
+ * @throws IOException
+ */
+ public NshmpNetcdfReader(String nshmpNetcdfFilename) throws IOException {
+
+ this.nshmpNetcdfFilename = nshmpNetcdfFilename;
+
+ // NSHMP 2018a data netCDF group path to data
+ nshmpBaseGroup = "/CONUS/2018/v1.1";
+
+ // Set netcdf-java logging level
+ // WARNING is default
+ // SEVERE disables warnings
+ logger = Logger.getLogger("ucar");
+ logger.setLevel(Level.SEVERE);
+
+ // Open netCDF file
+ // TODO: switch to try-with-resource block (solve errors when initializing
+ // final fields)
+ NetcdfDataset ncd = NetcdfDataset.openDataset(this.nshmpNetcdfFilename);
+
+ // TODO: handle metadata from netCDF file
+ // get root group and attributes, and attributes of subgroups
+
+ // TODO: get netCDF dimensions
+
+ // get target data group
+ Group targetGroup = ncd.findGroup(nshmpBaseGroup);
+
+ // get coordinate variables
+ Variable vVs30 = targetGroup.findVariable("vs30");
+ Variable vImts = targetGroup.findVariable("Imt");
+ Variable vlats = targetGroup.findVariable("lat");
+ Variable vlons = targetGroup.findVariable("lon");
+ Variable vImls = targetGroup.findVariable("Imls");
+ // TODO: hazard map variable will be renamed in netCDF file
+ Variable vhazardLevels = targetGroup.findVariable("Poe");
+ // or, for shared variables or dimensions:
+ // Variable vLat = targetGroup.findVariableOrInParent("lat");
+
+ // store coordinate variables in nshmpCoords
+ nshmpCoords = new NshmpNetcdfCoordinates(vVs30, vImts, vlats, vlons, vImls, vhazardLevels);
+
+ // Close NetcdfDataset
+ // TODO: avoid this with try-with-resource block
+ if (null != ncd) try {
+ ncd.close();
+ } catch (IOException ioe) {
+ logger.log(Level.SEVERE, "Failed trying to close " + this.nshmpNetcdfFilename, ioe);
+ }
+
+ }
+
+ /*
+ * Return the full set of hazard curves at the bounding grid points and the
+ * target Location. Intended for validation uses.
+ */
+ public static List<Map<SiteClass, Map<Imt, XySequence>>> getBoundingHazards(
+ NshmpNetcdfReader nshmpNCRD, Location site) {
+ BoundingHazards boundingHazards = new BoundingHazards(nshmpNCRD, site);
+
+ return boundingHazards.boundingHazardsList;
+ }
+
+ /*
+ * Return a Map<SiteClass, Map<Imt, XySequence>> with hazard curves at the
+ * specified Location.
+ */
+ public static Map<SiteClass, Map<Imt, XySequence>> getHazardAtSite(NshmpNetcdfReader nshmpNCRD,
+ Location site) {
+ List<Map<SiteClass, Map<Imt, XySequence>>> boundingHazardsList =
+ getBoundingHazards(nshmpNCRD, site);
+ return boundingHazardsList.get(4);
+ }
+
+ /*
+ * Return a single hazard curve for the specified Location, SiteClass, and
+ * Imt.
+ */
+ public static XySequence getHazardCurve(NshmpNetcdfReader nshmpNCRD, Location site, SiteClass sc,
+ Imt imt) {
+ Map<SiteClass, Map<Imt, XySequence>> hazardCurves = getHazardAtSite(nshmpNCRD, site);
+ return hazardCurves.get(sc).get(imt);
+ }
+
+ /*
+ * Container for dimensions and coordinate variables of nshmp netCDF file to
+ * facilitate indexing operations prior to data retrieval.
+ */
+ private class NshmpNetcdfCoordinates {
+
+ final int[] vs30s;
+ final List<SiteClass> siteClassEnums;
+
+ final double[] imtVals;
+ final List<Imt> imts;
+
+ final double[] lats;
+ final double[] lons;
+
+ final Map<SiteClass, Map<Imt, double[]>> imlMap;
+ final double[] hazardLevels;
+
+ final double maxLon;
+ final double minLon;
+ final double maxLat;
+ final double minLat;
+ final double deltaLon;
+ final double deltaLat;
+
+ final int nVs;
+ final int nImt;
+ final int nLat;
+ final int nLon;
+ final int nIml;
+ final int nHazardLevel;
+
+ /**
+ * @param vVs30s
+ * @param vImts
+ * @param vlats
+ * @param vlons
+ * @param vImls
+ * @param vHazardLevels
+ * @throws IOException
+ */
+ public NshmpNetcdfCoordinates(
+ Variable vVs30s,
+ Variable vImts,
+ Variable vlats,
+ Variable vlons,
+ Variable vImls,
+ Variable vHazardLevels) throws IOException {
+ // This bypasses the netCDF dimensions, but since we know what the
+ // variables and their dimensions should be, this is OK(???)
+
+ // read coordinate variables into java arrays
+ vs30s = (int[]) vVs30s.read().get1DJavaArray(DataType.INT);
+ imtVals = (double[]) vImts.read().get1DJavaArray(DataType.DOUBLE);;
+ lats = (double[]) vlats.read().get1DJavaArray(DataType.DOUBLE);;
+ lons = (double[]) vlons.read().get1DJavaArray(DataType.DOUBLE);;
+ hazardLevels = (double[]) vHazardLevels.read().get1DJavaArray(DataType.DOUBLE);
+
+ // assumes lons and lats are sorted ascending
+ maxLon = lons[lons.length - 1];
+ minLon = lons[0];
+ maxLat = lats[lats.length - 1];
+ minLat = lats[0];
+
+ // get lat/lon spacing --> this is currently a required attribute but is
+ // not used
+ deltaLon = (double) vlons.findAttribute("spacing").getNumericValue();
+ deltaLat = (double) vlats.findAttribute("spacing").getNumericValue();
+
+ nVs = vs30s.length;
+ nImt = imtVals.length;
+ nLat = lats.length;
+ nLon = lons.length;
+ nHazardLevel = hazardLevels.length;
+
+ // vImls has dimensions (vs30, Imt, Iml)
+ // alternatively get nIml from Dimension Iml
+ nIml = vImls.getDimension(2).getLength(); // Imls.length;
+
+ // convert Vs30<int> to SiteClass Enum
+ // TODO: site class should be stored as enum in netCDF file rather than
+ // vs30 value, so this will break:
+ siteClassEnums = Arrays.stream(vs30s)
+ .mapToObj(x -> mapVsToEnum2018(x))
+ .collect(Collectors.toUnmodifiableList());
+
+ // convert Imt<double> to Imt Enum
+ // TODO: Imt should be stored in netCDF as enum, so this will break:
+ imts = Arrays.stream(imtVals)
+ .mapToObj(x -> (x < 0.009) ? Imt.PGA : Imt.fromPeriod(x))
+ .collect(Collectors.toUnmodifiableList());
+
+ // Extract Imls to Map
+ // vImls is a 3-dimensional array with dims (vs30, Imt, Iml)
+ // Array ImlsArray = vImls.read();
+ // int[] imlDims = ImlsArray.getShape();
+
+ imlMap = mapImls(vImls);
+ }
+
+ /*
+ * validate target coordinates
+ */
+ void checkCoords(double lon, double lat) {
+ checkArgument(
+ (lon >= minLon && lon <= maxLon && lat >= minLat && lat <= maxLat),
+ String.format("Target coordinates out of range, %.3f <= lon < %.3f, %.3f <= lat <= %.3f",
+ minLon, maxLat, minLat, maxLat));
+ }
+
+ void checkCoords(Location targetSite) {
+ checkCoords(targetSite.longitude, targetSite.latitude);
+ }
+
+ /*
+ * convert 3D Iml variable (dimensions vs30, Imt, Iml) to map of Imls by
+ * SiteClass and Imt
+ *
+ * TODO: use MultiMap or SetMultiMap (etc.) to store unique IML sets? Could
+ * then also initialize the underlying XySequence objects for reading in the
+ * hazard curves...
+ */
+ private Map<SiteClass, Map<Imt, double[]>> mapImls(Variable vImls) {
+
+ // initialize
+ EnumMap<SiteClass, Map<Imt, double[]>> vsImtImlMap = Maps.newEnumMap(SiteClass.class);
+
+ for (int i = 0; i < siteClassEnums.size(); i++) {
+ SiteClass sc = siteClassEnums.get(i);
+
+ Map<Imt, double[]> imtImlMap = Maps.newEnumMap(Imt.class);
+ for (int j = 0; j < imts.size(); j++) {
+ Imt imt = imts.get(j);
+
+ // set origin and shape of double[] Imls to read
+ int[] origin = new int[] { i, j, 0 };
+ int[] shape = new int[] { 1, 1, nIml };
+
+ try {
+ imtImlMap.put(imt,
+ (double[]) vImls.read(origin, shape).reduce().get1DJavaArray(DataType.DOUBLE));
+ } catch (IOException | InvalidRangeException e) {
+ System.err.println("Failed read attempt for vImls with origin: " +
+ Arrays.toString(origin) + ", shape: " + Arrays.toString(shape));
+ e.printStackTrace();
+ }
+ }
+
+ vsImtImlMap.put(sc, imtImlMap);
+ }
+
+ return Maps.immutableEnumMap(vsImtImlMap);
+ }
+
+ private Location getLoc(int idxLon, int idxLat) {
+ return Location.create(lats[idxLat], lons[idxLon]);
+ }
+ }
+
+ /*
+ * Container for gridded hazard curves at four closest grid points to target
+ */
+ static class BoundingHazards {
+
+ final NshmpNetcdfReader ncrd;
+ final Location site;
+
+ private int idxLonLL;
+ private int idxLatLL;
+ private List<Location> boundingSites;
+
+ final double fracLon;
+ final double fracLat;
+
+ final List<Map<SiteClass, Map<Imt, XySequence>>> boundingHazardsList;
+ // final Map<SiteClass, Map<Imt, double[]>> targetHazards;
+
+ BoundingHazards(NshmpNetcdfReader ncrd, Location site) {
+ this.ncrd = ncrd;
+ this.site = site;
+
+ // validate target coordinates
+ ncrd.nshmpCoords.checkCoords(this.site);
+
+ // Compute indices for lower left bounding grid point
+ idxLonLL = getIdxLTEQ(ncrd.nshmpCoords.lons, this.site.longitude);
+ idxLatLL = getIdxLTEQ(ncrd.nshmpCoords.lats, this.site.latitude);
+
+ // Get bounding grid points: LL, UL, UR, LR
+ boundingSites = new ArrayList<Location>(4);
+ boundingSites.add(ncrd.nshmpCoords.getLoc(idxLonLL(), idxLatLL()));
+ boundingSites.add(ncrd.nshmpCoords.getLoc(idxLonUL(), idxLatUL()));
+ boundingSites.add(ncrd.nshmpCoords.getLoc(idxLonUR(), idxLatUR()));
+ boundingSites.add(ncrd.nshmpCoords.getLoc(idxLonLR(), idxLatLR()));
+
+ // Compute grid fractions to target point
+ fracLon = calcGridFrac(ncrd.nshmpCoords.lons, idxLonLL(), site.longitude);
+ fracLat = calcGridFrac(ncrd.nshmpCoords.lats, idxLatLL(), site.latitude);
+
+ boundingHazardsList = this.ncrd.extractHazardsAt(idxLonLL, idxLatLL);
+
+ // targetHazards = calcTargetHazards();
+ boundingHazardsList.add(calcTargetHazards());
+
+ }
+
+ private Map<SiteClass, Map<Imt, XySequence>> calcTargetHazards() {
+
+ // interpolate from LL to UL point
+ Map<SiteClass, Map<Imt, XySequence>> westTarget =
+ getTargetData(boundingHazardsList.get(0), boundingHazardsList.get(1), fracLat);
+ // interpolate from LR to UR point
+ Map<SiteClass, Map<Imt, XySequence>> eastTarget =
+ getTargetData(boundingHazardsList.get(3), boundingHazardsList.get(2), fracLat);
+
+ // do E-W interpolation
+ return getTargetData(westTarget, eastTarget, fracLon);
+
+ }
+
+ void dumpCoords() {
+ System.err.printf("%14s %14s %14s %14s %14s %14s %s\n", "Point", "LL", "UL", "UR", "LR",
+ "Target", "Frac");
+ System.err.printf("%14s %14.5f %14.5f %14.5f %14.5f %14.5f %.8f\n", "Lat:",
+ boundingSites.get(0).latitude,
+ boundingSites.get(1).latitude,
+ boundingSites.get(2).latitude,
+ boundingSites.get(3).latitude,
+ site.latitude,
+ fracLat);
+ System.err.printf("%14s %14.5f %14.5f %14.5f %14.5f %14.5f %.8f\n", "Lon:",
+ boundingSites.get(0).longitude,
+ boundingSites.get(1).longitude,
+ boundingSites.get(2).longitude,
+ boundingSites.get(3).longitude,
+ site.longitude,
+ fracLon);
+
+ }
+
+ void dumpBoundingPlusTarget(SiteClass sc, Imt imt) {
+ System.err.printf("Results for:\n");
+ System.err.printf(" SiteClass: %2s, %d m/s\n", sc.toString(), mapSiteClassToVs30(sc));
+ System.err.printf(" IMT: %s, %s\n", imt.name(), imt.period());
+
+ dumpCoords();
+ System.err.printf("%14s\n", "Iml");
+ for (int i = 0; i < ncrd.nshmpCoords.nIml; i++) {
+ // System.err.printf("%14d %14d %14d %14d %14d %14d\n",
+ // (long) ncrd.nshmpCoords.imlMap.get(sc).get(imt)[i],
+ // (long) boundingHazardsList.get(0).get(sc).get(imt).y(i),
+ // (long) boundingHazardsList.get(1).get(sc).get(imt).y(i),
+ // (long) boundingHazardsList.get(2).get(sc).get(imt).y(i),
+ // (long) boundingHazardsList.get(3).get(sc).get(imt).y(i),
+ // (long) boundingHazardsList.get(4).get(sc).get(imt).y(i));
+ System.err.printf("%14.5f %14.6e %14.6e %14.6e %14.6e %14.6e\n",
+ ncrd.nshmpCoords.imlMap.get(sc).get(imt)[i],
+ boundingHazardsList.get(0).get(sc).get(imt).y(i),
+ boundingHazardsList.get(1).get(sc).get(imt).y(i),
+ boundingHazardsList.get(2).get(sc).get(imt).y(i),
+ boundingHazardsList.get(3).get(sc).get(imt).y(i),
+ boundingHazardsList.get(4).get(sc).get(imt).y(i));
+ }
+
+ }
+
+ void dumpBoundingPlusTarget(int idxSc, int idxImt) {
+ dumpBoundingPlusTarget(
+ ncrd.nshmpCoords.siteClassEnums.get(idxSc),
+ ncrd.nshmpCoords.imts.get(idxImt));
+ }
+
+ int idxLonLL() {
+ return idxLonLL;
+ }
+
+ int idxLatLL() {
+ return idxLatLL;
+ }
+
+ int idxLonUL() {
+ return idxLonLL;
+ }
+
+ int idxLatUL() {
+ return idxLatLL + 1;
+ }
+
+ int idxLonUR() {
+ return idxLonLL + 1;
+ }
+
+ int idxLatUR() {
+ return idxLatLL + 1;
+ }
+
+ int idxLonLR() {
+ return idxLonLL + 1;
+ }
+
+ int idxLatLR() {
+ return idxLatLL;
+ }
+
+ }
+
+ public static void main(String[] args) {
+
+ String filename = args[0];
+
+ double targetLon = -105.23;
+ double targetLat = 39.2;
+ // double targetLon = -65.0;
+ // double targetLat = 50.0;
+ Location targetSite = Location.create(targetLat, targetLon);
+
+ // initialize reader
+ NshmpNetcdfReader nshmpNCDR = null;
+ try {
+ System.err.println("attempting to open file ");
+ nshmpNCDR = new NshmpNetcdfReader(filename);
+ } catch (IOException e) {
+ System.err.println("Failed to initialize NshmpNetcdfReader");
+ e.printStackTrace();
+ }
+
+ // test Iml map - are Imls consistent for a given Imt across SiteClass?
+ if (checkConsistentImls(nshmpNCDR.nshmpCoords.imlMap, nshmpNCDR.nshmpCoords.siteClassEnums,
+ nshmpNCDR.nshmpCoords.imts)) {
+ System.err.println("Iml sets are consistent for each Imt across all site classes\n");
+ }
+
+ BoundingHazards boundingHazards = new BoundingHazards(nshmpNCDR, targetSite);
+
+ for (int iSc = 0; iSc < nshmpNCDR.nshmpCoords.nVs; iSc++) {
+ for (int iImt = 0; iImt < nshmpNCDR.nshmpCoords.nImt; iImt++) {
+ System.err.println("\n");
+ boundingHazards.dumpBoundingPlusTarget(mapVsToEnum2018(nshmpNCDR.nshmpCoords.vs30s[iSc]),
+ nshmpNCDR.nshmpCoords.imts.get(iImt));
+ }
+ }
+ // System.err.println("\n");
+ // boundingHazards.dumpBoundingPlusTarget(mapVsToEnum2018(150), Imt.PGA);
+ System.err.println("\n** done **");
+ }
+
+ /*
+ * Return hazard curves for four closest grid points as a List of:
+ * Map<SiteClass, Map<Imt, XySequence(iml,hazard)>>
+ *
+ * List order is clockwise from lower left corner: LL, UL, UR, LR, [T] with an
+ * empty slot for the interpolated target hazards
+ */
+ private List<Map<SiteClass, Map<Imt, XySequence>>> extractHazardsAt(int idxLonLL, int idxLatLL) {
+
+ // initialize list
+ List<Map<SiteClass, Map<Imt, XySequence>>> boundingHazardMaps =
+ new ArrayList<Map<SiteClass, Map<Imt, XySequence>>>(5);
+
+ try (NetcdfDataset ncd = NetcdfDataset.openDataset(nshmpNetcdfFilename)) {
+
+ Group targetGroup = ncd.findGroup(nshmpBaseGroup);
+
+ // TODO: rename variable in netCDF
+ Variable vHazards = targetGroup.findVariable("AEPs");
+
+ // set up origin and shape arrays for reading hazard curves at four
+ // bounding
+ // (lon,lat) grid points
+ int[] origin = new int[] { 0, 0, idxLatLL, idxLonLL, 0 };
+ int[] shape = new int[] { nshmpCoords.nVs, nshmpCoords.nImt, 2, 2, nshmpCoords.nIml };
+
+ // read data into Array for bounding grid points
+ // System.err.println("reading hazards for four points");
+ Array aHazards = vHazards.read(origin, shape);
+
+ // Array aHazards now has shape [nVs,nImt,2,2,nIml]
+ // ...so origin will now be [0,0,0,0,0] for LL grid point
+ // ...and shape of requested array is [nVs,nImt,1,1,nIml]
+
+ // System.err.println(aHazards.shapeToString());
+ // Array aHazards is size 2 on the lon and lat dimensions
+ shape[2] = 1;
+ shape[3] = 1;
+
+ // TODO: XySequence instead of double[]
+
+ // Put data into hazard map for LL point
+ origin[2] = 0; // lat index position
+ origin[3] = 0; // lon index position
+ // System.err.println("getting LL hazards");
+ boundingHazardMaps.add(mapHazardsFromArray(aHazards.section(origin, shape)));
+ // Put data into hazard map for UL point
+ origin[2] = 1; // lat index position
+ origin[3] = 0; // lon index position
+ // System.err.println("getting UL hazards");
+ boundingHazardMaps.add(mapHazardsFromArray(aHazards.section(origin, shape)));
+ // Put data into hazard map for UR point
+ origin[2] = 1; // lat index position
+ origin[3] = 1; // lon index position
+ // System.err.println("getting UR hazards");
+ boundingHazardMaps.add(mapHazardsFromArray(aHazards.section(origin, shape)));
+ // Put data into hazard map for LR point
+ origin[2] = 0; // lat index position
+ origin[3] = 1; // lon index position
+ // System.err.println("getting LR hazards");
+ boundingHazardMaps.add(mapHazardsFromArray(aHazards.section(origin, shape)));
+
+ // // read data into Array (using Variable.read() for each hazard curve)
+ // THIS IS SLOW
+ // // TODO: XySequence instead of double[]
+ // // TODO: read data from variable ONCE!!! convert Array to maps
+ // // initialize list
+ // List<Map<SiteClass, Map<Imt, double[]>>> boundingHazardMaps =
+ // new ArrayList<Map<SiteClass, Map<Imt, double[]>>>(4);
+ // // Read data into hazard map for LL point
+ // System.err.println("getting LL hazards");
+ // boundingHazardMaps.add(mapHazards(vHazards, idxLonLL, idxLatLL));
+ // // Read data into hazard map for UL point
+ // System.err.println("getting UL hazards");
+ // boundingHazardMaps.add(mapHazards(vHazards, idxLonLL, idxLatLL + 1));
+ // // Read data into hazard map for UR point
+ // System.err.println("getting UR hazards");
+ // boundingHazardMaps.add(mapHazards(vHazards, idxLonLL + 1, idxLatLL +
+ // 1));
+ // // Read data into hazard map for LR point
+ // System.err.println("getting LR hazards");
+ // boundingHazardMaps.add(mapHazards(vHazards, idxLonLL + 1, idxLatLL));
+
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ } catch (InvalidRangeException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ // interpolate hazards to target point
+ return boundingHazardMaps;
+
+ }
+
+ /*
+ * TODO: attempt to calculate index
+ *
+ * possibly as NshmpNetcdfCoordinates.calcIdxLTEQ()
+ */
+
+ /*
+ * Read hazard curves from netCDF variable into map of hazards by SiteClass
+ * and Imt
+ *
+ * TODO: if target is on a grid point (or on a grid lat or lon), no need to
+ * read 4 bounding points ?
+ */
+ private Map<SiteClass, Map<Imt, XySequence>> mapHazardsFromArray(Array aHazards) {
+ // aHazards has had its lat and lon dimensions reduced (so it now is rank 3)
+ // aHazards[SiteClass, Imt, Iml]
+
+ // initialize
+ EnumMap<SiteClass, Map<Imt, XySequence>> vsImtHazardMap = Maps.newEnumMap(SiteClass.class);
+
+ for (int iSc = 0; iSc < nshmpCoords.siteClassEnums.size(); iSc++) {
+ SiteClass sc = nshmpCoords.siteClassEnums.get(iSc);
+
+ Map<Imt, XySequence> imtHazardMap = Maps.newEnumMap(Imt.class);
+ for (int iImt = 0; iImt < nshmpCoords.imts.size(); iImt++) {
+ Imt imt = nshmpCoords.imts.get(iImt);
+
+ // set origin and shape of double[] hazards to read
+ int[] origin = new int[] { iSc, iImt, 0 };
+ int[] shape = new int[] { 1, 1, nshmpCoords.nIml };
+
+ // try block needed for sectioning Array
+ try {
+ imtHazardMap.put(imt,
+ XySequence.create(
+ nshmpCoords.imlMap.get(sc).get(imt),
+ (double[]) aHazards.section(origin, shape).reduce()
+ .get1DJavaArray(DataType.DOUBLE)));
+ } catch (InvalidRangeException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+
+ }
+
+ vsImtHazardMap.put(sc, imtHazardMap);
+ }
+
+ return Maps.immutableEnumMap(vsImtHazardMap);
+ }
+
+ /*
+ * Read hazard curves from netCDF variable into map of hazards by SiteClass
+ * and Imt
+ *
+ * TODO: if target is on a grid point (or on a grid lat or lon), no need to
+ * read 4 bounding points
+ */
+ private Map<SiteClass, Map<Imt, double[]>> mapHazards(Variable vHazards, int idxLon, int idxLat) {
+
+ // initialize
+ EnumMap<SiteClass, Map<Imt, double[]>> vsImtHazardMap = Maps.newEnumMap(SiteClass.class);
+
+ for (int iSc = 0; iSc < nshmpCoords.siteClassEnums.size(); iSc++) {
+ SiteClass sc = nshmpCoords.siteClassEnums.get(iSc);
+
+ Map<Imt, double[]> imtHazardMap = Maps.newEnumMap(Imt.class);
+ for (int iImt = 0; iImt < nshmpCoords.imts.size(); iImt++) {
+ Imt imt = nshmpCoords.imts.get(iImt);
+
+ // set origin and shape of double[] hazards to read
+ int[] origin = new int[] { iSc, iImt, idxLat, idxLon, 0 };
+ int[] shape = new int[] { 1, 1, 1, 1, nshmpCoords.nIml };
+
+ try {
+ imtHazardMap.put(imt,
+ (double[]) vHazards.read(origin, shape).reduce().get1DJavaArray(DataType.DOUBLE));
+ } catch (IOException | InvalidRangeException e) {
+ System.err.println("Failed read attempt for vHazards with origin: " +
+ Arrays.toString(origin) + ", shape: " + Arrays.toString(shape));
+ e.printStackTrace();
+ }
+
+ }
+
+ vsImtHazardMap.put(sc, imtHazardMap);
+ }
+
+ return Maps.immutableEnumMap(vsImtHazardMap);
+ }
+
+ /*
+ * find index of first element in a (sorted ascending) that is less than or
+ * equal to target value t. If target value is equal to the maximum value in a
+ * (the last element), an index of a.length - 1 is returned.
+ */
+ private static int getIdxLTEQ(double[] a, double t) {
+ // assumes array is in sorted order (a[i] < a[i+1])
+ // make sure target is within the range of the array
+ double tol = 0.000001;
+ int n = a.length;
+ if (t < a[0] || t > a[n - 1]) {
+ // should never get here thanks to NshmpNetcdfCoordinates.checkCoords()
+ throw new IllegalArgumentException(
+ String.format("Target outside of valid range: %.4f <= t <= %4f", a[0], a[n - 1]));
+ }
+ // if (t == a[0]) {
+ if (DoubleMath.fuzzyEquals(a[0], t, tol)) {
+ return 0;
+ }
+ // if (t == a[n - 1]) {
+ if (DoubleMath.fuzzyEquals(a[n - 1], t, tol)) {
+ return n - 2; // return second to last index number
+ }
+
+ int idx = Arrays.binarySearch(a, t);
+ if (idx < 0) {
+ // "exact" match not found, so use index of first value less than target
+ // this is insertion_point - 1
+ // returned idx = -insertion_point - 1
+ idx = -1 * (idx + 1) - 1;
+ // array[idx] <= target
+ }
+ return idx;
+ }
+
+ /*
+ * Calculate fractional distance from a1 to t, between a1 and a2
+ */
+ private static double calcFrac(double a1, double a2, double t) {
+ double tol = 0.00001;
+ double frac = 0.0;
+ if (Math.abs(t - a1) < tol) {
+ // target value == a1
+ frac = 0.0;
+ } else if (Math.abs(t - a2) < tol) {
+ // target value == a2
+ frac = 1.0;
+ } else {
+ // calculate fractional distance to t between a[i] and a[i+1]
+ frac = (t - a1) / (a2 - a1);
+ }
+ return frac;
+ }
+
+ /*
+ * Calculate fractional distance from a[i] to t, between a[i] and a[i+1]
+ */
+ private static double calcGridFrac(double[] a, int i, double t) {
+ return calcFrac(a[i], a[i + 1], t);
+ }
+
+ /*
+ * Get data for target point
+ *
+ * @param d1 data at first point (p1)
+ *
+ * @param d2 data at second point (p2)
+ *
+ * @param frac fractional distance between p1 and p2 to target point
+ */
+ private static Map<SiteClass, Map<Imt, XySequence>> getTargetData(
+ Map<SiteClass, Map<Imt, XySequence>> d1,
+ Map<SiteClass, Map<Imt, XySequence>> d2,
+ double frac) {
+ // do we need better checking here? or is it safe to assume that every
+ // Map<SiteClass, Map<Imt,double[]>> passed in is consistent?
+ if (d1.size() != d2.size()) {
+ throw new IllegalArgumentException("Array size disagreement, cannot interpolate");
+ }
+ Map<SiteClass, Map<Imt, XySequence>> tMap;
+ if (frac == 0.0) {
+ // target is the same as d1
+ tMap = d1;
+ } else if (frac == 1.0) {
+ // target is the same as d2
+ tMap = d2;
+ } else {
+ tMap = linearInterpolate(d1, d2, frac);
+ }
+ return tMap;
+ }
+
+ /*
+ * Linear interpolation of data values to a target point
+ *
+ * TODO: use XySequence.copyOf(), streams
+ */
+ private static Map<SiteClass, Map<Imt, XySequence>> linearInterpolate(
+ Map<SiteClass, Map<Imt, XySequence>> v1,
+ Map<SiteClass, Map<Imt, XySequence>> v2,
+ double frac) {
+ // return v1 * (1 - frac) + v2 * frac
+ // DoubleData routines add and multiply in place, we don't want to modify
+ // the original data here
+ if (v1.size() != v2.size()) {
+ throw new IllegalArgumentException("Array size disagreement, cannot interpolate");
+ }
+
+ Map<SiteClass, Map<Imt, XySequence>> tMap = Maps.newEnumMap(SiteClass.class);
+
+ for (SiteClass sc : v1.keySet()) {
+ Map<Imt, XySequence> imtHazards = Maps.newEnumMap(Imt.class);
+
+ for (Imt imt : v1.get(sc).keySet()) {
+ double[] v1Haz = v1.get(sc).get(imt).yValues().toArray();
+ double[] v2Haz = v2.get(sc).get(imt).yValues().toArray();
+ double[] t = new double[v1Haz.length];
+ for (int i = 0; i < v1Haz.length; i++) {
+ t[i] = v1Haz[i] * (1 - frac) + v2Haz[i] * frac;
+ }
+ imtHazards.put(imt, XySequence.create(v1.get(sc).get(imt).xValues().toArray(), t));
+ }
+ tMap.put(sc, imtHazards);
+ }
+ return tMap;
+ }
+
+ /*
+ * check that sets of Iml are consistent for a given Imt across all SiteClass
+ */
+ private static boolean checkConsistentImls(Map<SiteClass, Map<Imt, double[]>> imlMap,
+ List<SiteClass> siteClasses, List<Imt> imts) {
+
+ boolean allEqual = true;
+
+ // System.err.println("\n\n");
+ for (Imt imt : imts) {
+ // System.err.println("Checking Imt " + imt.toString());
+
+ double[] firstImls = new double[1];
+ SiteClass firstSc = null;
+ for (SiteClass sc : siteClasses) {
+ if (firstImls.length == 1) {
+ firstImls = imlMap.get(sc).get(imt);
+ firstSc = sc;
+ continue;
+ }
+ boolean imlsDiffer = false;
+ double[] theseImls = imlMap.get(sc).get(imt);
+ for (int i = 0; i < firstImls.length; i++) {
+ if (DoubleMath.fuzzyEquals(firstImls[i], theseImls[i], 1e-9)) {
+ continue;
+ }
+ imlsDiffer = true;
+ allEqual = false;
+ break;
+ }
+ // if (imlsDiffer) {
+ // // Imls differ for imt between lastSc and sc
+ // System.err.println("Iml set differs, " + firstSc.toString() + " vs. "
+ // + sc.toString());
+ // System.err.println(" " + Arrays.toString(firstImls));
+ // System.err.println(" " + Arrays.toString(theseImls));
+ //
+ // }
+ }
+ }
+ return allEqual;
+ }
+
+ /**
+ * This should be imported. For now, it is copied from
+ * nshmp-haz-v2/src/gov.usgs.earthquake.nshmp.site.NehrpSiteClass.java
+ *
+ * Placeholder enum for likely move to Nehrp site class identifier instead of
+ * Vs30.
+ *
+ * <p>These site class identifiers map to NEHRP site clases, but the intent is
+ * that they can be used more generally for models in other parts of the world
+ * where the GMMs are not necessarily parameterized in terms of vs30 to define
+ * site response. For instance, NZ/JP site classes might use A, B, C, and D as
+ * a proxy for the local I, II, III, and IV identifiers. In the U.S., models
+ * will need to specify the Vs30 value that each site class corresponds to.
+ * Although the values were consistent over prior models, now that multiple
+ * site classes are supported (in 2018) across the entire U.S., there have
+ * been changes proposed for balloting by the BSSC to make the Vs30
+ * definitions of site classes consistent in how they are calculated.
+ *
+ * @author Peter Powers
+ */
+ enum SiteClass {
+
+ /*
+ * Notes on calculation of Vs30 for site class:
+ *
+ * Question: Why is it that the soil shear wave velocity shown in the
+ * Unified Hazard Tool is not equal to the average of the values shown in
+ * ASCE 7-10 table 20.3-1?
+ *
+ * For instance: 259 m/s (Site Class D), from the Unified Hazard Tool, is
+ * not equal to (600 ft/s + 1200 ft/s)/2 * .3048 = 274 m/s
+ *
+ * Answer (Sanaz): we take the geometric mean: sqrt(1200*600)*0.3048 =
+ * 258.6314 , which rounds to 259m/s.
+ *
+ *
+ */
+
+ /* OLD Vs30, NEW Vs30 */
+
+ /* 2000 2000 */
+ A,
+
+ /* 1500 1500 (new) */
+ AB,
+
+ /* 1150 1080 */
+ B,
+
+ /* 760 760 */
+ BC,
+
+ /* 537 530 */
+ C,
+
+ /* 360 365 */
+ CD,
+
+ /* 259 260 */
+ D,
+
+ /* 180 185 */
+ DE,
+
+ /* 150 150 (new) */
+ E,
+
+ ;
+ }
+
+ static SiteClass mapVsToEnum2018(int vs) {
+ // vs30 = 150, 185, 260, 365, 530, 760, 1080, 1500 ;
+ switch (vs) {
+ case 150:
+ return SiteClass.E;
+ case 185:
+ return SiteClass.DE;
+ case 260:
+ return SiteClass.D;
+ case 365:
+ return SiteClass.CD;
+ case 530:
+ return SiteClass.C;
+ case 760:
+ return SiteClass.BC;
+ case 1080:
+ return SiteClass.B;
+ case 1500:
+ return SiteClass.AB;
+ default:
+ throw new IllegalArgumentException(
+ String.format("Invalid Vs30, no matching 2018 SiteClass: %d", vs));
+ }
+ }
+
+ static int mapSiteClassToVs30(SiteClass sc) {
+ switch (sc) {
+ case A:
+ return 2000;
+ case AB:
+ return 1500;
+ case B:
+ return 1080;
+ case BC:
+ return 760;
+ case C:
+ return 530;
+ case CD:
+ return 365;
+ case D:
+ return 260;
+ case DE:
+ return 185;
+ case E:
+ return 150;
+ default:
+ throw new IllegalArgumentException(
+ String.format("Invalid SiteClass %s", sc.toString()));
+ }
+ }
+}
diff --git a/src/main/resources/eclipse.importorder b/src/main/resources/eclipse.importorder
deleted file mode 100644
index 6cc3df2..0000000
--- a/src/main/resources/eclipse.importorder
+++ /dev/null
@@ -1,5 +0,0 @@
-#Organize Import Order
-3=com
-2=org
-1=javax
-0=java
diff --git a/src/main/resources/nshmp.eclipse-format.xml b/src/main/resources/nshmp.eclipse-format.xml
deleted file mode 100644
index 181dbd1..0000000
--- a/src/main/resources/nshmp.eclipse-format.xml
+++ /dev/null
@@ -1,916 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<profiles version="13">
- <profile kind="CodeFormatterProfile" name="nshmp" version="13">
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_after_ellipsis"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_enum_declarations"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_annotation_declaration"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_allocation_expression"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_at_in_annotation_type_declaration"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.parentheses_positions_in_for_statment"
- value="common_lines" />
- <setting
- id="org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries"
- value="true" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_parameters"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_package"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.parentheses_positions_in_method_invocation"
- value="common_lines" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.blank_lines_after_imports"
- value="1" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_while"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_method_declaration_throws"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.parentheses_positions_in_switch_statement"
- value="common_lines" />
- <setting
- id="org.eclipse.jdt.core.formatter.comment.format_javadoc_comments"
- value="true" />
- <setting id="org.eclipse.jdt.core.formatter.indentation.size"
- value="2" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_after_postfix_operator"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.parentheses_positions_in_enum_constant_declaration"
- value="common_lines" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_increments"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_arguments"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_inits"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_anonymous_type_declaration"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_for"
- value="insert" />
- <setting id="org.eclipse.jdt.core.formatter.disabling_tag"
- value="@formatter:off" />
- <setting
- id="org.eclipse.jdt.core.formatter.continuation_indentation"
- value="2" />
- <setting
- id="org.eclipse.jdt.core.formatter.alignment_for_enum_constants"
- value="81" />
- <setting
- id="org.eclipse.jdt.core.formatter.blank_lines_before_imports"
- value="1" />
- <setting
- id="org.eclipse.jdt.core.formatter.blank_lines_after_package"
- value="1" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_after_binary_operator"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_local_declarations"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.parentheses_positions_in_if_while_statement"
- value="common_lines" />
- <setting
- id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant"
- value="16" />
- <setting
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- id="org.eclipse.jdt.core.formatter.comment.indent_root_tags"
- value="true" />
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- value="true" />
- <setting id="org.eclipse.jdt.core.formatter.enabling_tag"
- value="@formatter:on" />
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- id="org.eclipse.jdt.core.formatter.insert_space_after_closing_brace_in_block"
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- id="org.eclipse.jdt.core.formatter.comment.count_line_length_from_starting_position"
- value="false" />
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- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line"
- value="false" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_field"
- value="insert" />
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- value="insert" />
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- value="common_lines" />
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- id="org.eclipse.jdt.core.formatter.insert_space_between_empty_braces_in_array_initializer"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_case"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_local_declarations"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_annotation_type_declaration"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_reference"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_method_declaration"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.wrap_outer_expressions_when_nested"
- value="true" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_after_closing_paren_in_cast"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.brace_position_for_enum_constant"
- value="end_of_line" />
- <setting
- id="org.eclipse.jdt.core.formatter.brace_position_for_type_declaration"
- value="end_of_line" />
- <setting
- id="org.eclipse.jdt.core.formatter.blank_lines_before_package"
- value="0" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_for"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_synchronized"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_increments"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation_type_member_declaration"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.alignment_for_expressions_in_for_loop_header"
- value="0" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_while"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_enum_constant"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_explicitconstructorcall_arguments"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_annotation"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_parameters"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_constant_header"
- value="true" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_after_lambda_arrow"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_constructor_declaration"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_throws"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.join_lines_in_comments"
- value="true" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_parameters"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_question_in_conditional"
- value="insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.comment.indent_parameter_description"
- value="false" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_new_line_before_finally_in_try_statement"
- value="do not insert" />
- <setting id="org.eclipse.jdt.core.formatter.tabulation.char"
- value="space" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_field_declarations"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.blank_lines_between_import_groups"
- value="1" />
- <setting id="org.eclipse.jdt.core.formatter.lineSplit"
- value="100" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_annotation"
- value="do not insert" />
- <setting
- id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_switch"
- value="insert" />
- </profile>
-</profiles>
--
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