diff --git a/src/main/java/gov/usgs/earthquake/nshmp/netcdf/Netcdf.java b/src/main/java/gov/usgs/earthquake/nshmp/netcdf/Netcdf.java
deleted file mode 100644
index 048b8bcfd52e099363a5962f43a45bc6e3f31ab4..0000000000000000000000000000000000000000
--- a/src/main/java/gov/usgs/earthquake/nshmp/netcdf/Netcdf.java
+++ /dev/null
@@ -1,60 +0,0 @@
-package gov.usgs.earthquake.nshmp.netcdf;
-
-import java.io.IOException;
-import java.nio.file.Path;
-import java.util.List;
-import java.util.Map;
-
-import gov.usgs.earthquake.nshmp.data.XySequence;
-import gov.usgs.earthquake.nshmp.geo.Location;
-import gov.usgs.earthquake.nshmp.gmm.Imt;
-
-public interface Netcdf {
-
- /**
- * Returns a {@code NetCdf} reader for 2018 hazard curves.
- *
- * @param path The path to the 2018 Netcdf hazard file
- * @throws IOException
- */
- public static Netcdf create2018Reader(Path path) {
- return new Netcdf2018Reader(path);
- }
-
- /**
- * Returns the Netcdf dimensions and coordinate variables.
- */
- NetcdfCoordinates coordinates();
-
- /**
- * Returns the path to the Netcdf file.
- */
- Path path();
-
- /**
- * Return the full set of hazard curves at the bounding grid points and the
- * target Location. Intended for validation uses.
- *
- * @param site The location to get bouning hazards
- */
- List<Map<SiteClass, Map<Imt, XySequence>>> boundingHazards(Location site);
-
- /**
- * Return a Map<SiteClass, Map<Imt, XySequence>> with hazard curves at the
- * specified Location.
- *
- * @param site The site to get the hazard curves
- */
- Map<SiteClass, Map<Imt, XySequence>> hazard(Location site);
-
- /**
- * Return a single hazard curve for the specified Location, SiteClass, and
- * Imt.
- *
- * @param site The site to get the hazard curves
- * @param siteClass The site class
- * @param imt The IMT
- */
- XySequence hazard(Location site, SiteClass siteClass, Imt imt);
-
-}
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/netcdf/NshmGroup.java b/src/main/java/gov/usgs/earthquake/nshmp/netcdf/NshmGroup.java
new file mode 100644
index 0000000000000000000000000000000000000000..b6470018837709aa169efb38df4104774e019b2b
--- /dev/null
+++ b/src/main/java/gov/usgs/earthquake/nshmp/netcdf/NshmGroup.java
@@ -0,0 +1,21 @@
+package gov.usgs.earthquake.nshmp.netcdf;
+
+public enum NshmGroup {
+
+ NSHM_CONUS_2018("/CONUS/2018/v1.1");
+
+ private final String baseGroup;
+
+ private NshmGroup(String baseGroup) {
+ this.baseGroup = baseGroup;
+ }
+
+ /**
+ * Returns the Netcdf target base group to read.
+ */
+ @Override
+ public String toString() {
+ return baseGroup;
+ }
+
+}
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/netcdf/Netcdf2018Reader.java b/src/main/java/gov/usgs/earthquake/nshmp/netcdf/NshmNetcdfReader.java
similarity index 57%
rename from src/main/java/gov/usgs/earthquake/nshmp/netcdf/Netcdf2018Reader.java
rename to src/main/java/gov/usgs/earthquake/nshmp/netcdf/NshmNetcdfReader.java
index 0e482fdb1bc193223d6c638896110e85b3fae7e2..6cbdd8d62f23031955771b7a00367ad953b62bc9 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/netcdf/Netcdf2018Reader.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/netcdf/NshmNetcdfReader.java
@@ -5,10 +5,14 @@ import java.nio.file.Files;
import java.nio.file.Path;
import java.util.List;
import java.util.Map;
+import java.util.logging.Level;
+import java.util.logging.Logger;
import gov.usgs.earthquake.nshmp.data.XySequence;
import gov.usgs.earthquake.nshmp.geo.Location;
import gov.usgs.earthquake.nshmp.gmm.Imt;
+import gov.usgs.earthquake.nshmp.netcdf.reader.BoundingHazards;
+import gov.usgs.earthquake.nshmp.netcdf.reader.NetcdfCoordinates;
import ucar.nc2.dataset.NetcdfDataset;
@@ -33,14 +37,21 @@ import ucar.nc2.dataset.NetcdfDataset;
*
* @author U.S. Geological Survey
*/
-class Netcdf2018Reader implements Netcdf {
+public class NshmNetcdfReader {
- private static final String BASE_GROUP = "/CONUS/2018/v1.1";
+ private static final Logger LOGGER = Logger.getLogger("ucar");
private final Path path;
+ private final NshmGroup nshmGroup;
private final NetcdfCoordinates coords;
- Netcdf2018Reader(Path path) {
+ static {
+ /* Update ucar logger */
+ LOGGER.setLevel(Level.SEVERE);
+ }
+
+ public NshmNetcdfReader(NshmGroup nshmGroup, Path path) {
+ this.nshmGroup = nshmGroup;
this.path = path;
if (Files.notExists(path)) {
@@ -52,34 +63,62 @@ class Netcdf2018Reader implements Netcdf {
// - Handle metadata from netCDF file get root group and
// attributes, and attributes of subgroups
// - Get netCDF dimensions
- var targetGroup = ncd.findGroup(BASE_GROUP);
+ var targetGroup = ncd.findGroup(nshmGroup.toString());
coords = new NetcdfCoordinates(targetGroup);
} catch (IOException e) {
throw new RuntimeException("Could not read Netcdf file [" + path + " ]");
}
}
- @Override
+ /**
+ * Returns the NSHM NetCDF group
+ */
+ public NshmGroup nshmGroup() {
+ return nshmGroup;
+ }
+
+ /**
+ * Returns the NetCDF dimensions and coordinate variables.
+ */
public NetcdfCoordinates coordinates() {
return coords;
}
- @Override
+ /**
+ * Returns the path to the NetCDF file.
+ */
public Path path() {
return path;
}
- @Override
+ /**
+ * Return the full set of hazard curves at the bounding grid points and the
+ * target Location. Intended for validation uses.
+ *
+ * @param site The location to get bounding hazards
+ */
public List<Map<SiteClass, Map<Imt, XySequence>>> boundingHazards(Location site) {
- return BoundingHazards.boundingHazards(this, site, BASE_GROUP);
+ return BoundingHazards.boundingHazards(this, site);
}
- @Override
+ /**
+ * Return a Map<SiteClass, Map<Imt, XySequence>> with hazard curves at the
+ * specified Location.
+ *
+ * @param site The site to get the hazard curves
+ */
public Map<SiteClass, Map<Imt, XySequence>> hazard(Location site) {
return boundingHazards(site).get(4);
}
- @Override
+ /**
+ * Return a single hazard curve for the specified Location, SiteClass, and
+ * Imt.
+ *
+ * @param site The site to get the hazard curves
+ * @param siteClass The site class
+ * @param imt The IMT
+ */
public XySequence hazard(Location site, SiteClass siteClass, Imt imt) {
return hazard(site).get(siteClass).get(imt);
}
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/netcdf/BoundingHazards.java b/src/main/java/gov/usgs/earthquake/nshmp/netcdf/reader/BoundingHazards.java
similarity index 87%
rename from src/main/java/gov/usgs/earthquake/nshmp/netcdf/BoundingHazards.java
rename to src/main/java/gov/usgs/earthquake/nshmp/netcdf/reader/BoundingHazards.java
index f89e2cf7898fb92411ac7209c331636b7d78ff50..769db9dcd5c805f1e409c33ad65c7bba58025d6b 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/netcdf/BoundingHazards.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/netcdf/reader/BoundingHazards.java
@@ -1,4 +1,4 @@
-package gov.usgs.earthquake.nshmp.netcdf;
+package gov.usgs.earthquake.nshmp.netcdf.reader;
import java.io.IOException;
import java.util.ArrayList;
@@ -11,7 +11,9 @@ import com.google.common.collect.Maps;
import gov.usgs.earthquake.nshmp.data.XySequence;
import gov.usgs.earthquake.nshmp.geo.Location;
import gov.usgs.earthquake.nshmp.gmm.Imt;
-import gov.usgs.earthquake.nshmp.netcdf.NetcdfUtils.Key;
+import gov.usgs.earthquake.nshmp.netcdf.NshmNetcdfReader;
+import gov.usgs.earthquake.nshmp.netcdf.SiteClass;
+import gov.usgs.earthquake.nshmp.netcdf.reader.NetcdfUtils.Key;
import ucar.ma2.Array;
import ucar.ma2.DataType;
@@ -23,29 +25,38 @@ import ucar.nc2.dataset.NetcdfDataset;
/*
* Container for gridded hazard curves at four closest grid points to target
*/
-class BoundingHazards {
+public class BoundingHazards {
- final Netcdf netcdf;
- final String baseGroup;
- final NetcdfCoordinates coords;
+ private final NshmNetcdfReader netcdf;
+ private final NetcdfCoordinates coords;
+ private List<Map<SiteClass, Map<Imt, XySequence>>> boundingHazards;
- private int idxLonLL;
- private int idxLatLL;
-
- final List<Map<SiteClass, Map<Imt, XySequence>>> boundingHazards;
-
- private BoundingHazards(Netcdf netcdf, Location site, String baseGroup) {
+ private BoundingHazards(NshmNetcdfReader netcdf, Location site) {
this.netcdf = netcdf;
- this.baseGroup = baseGroup;
this.coords = netcdf.coordinates();
+ coords.contains(site);
+ setBoundingHazards(site);
+ }
- coords.checkCoords(site);
+ /**
+ * Returns the bounding hazards at four closet grid points to target.
+ *
+ * @param netcdf The {@code Netcdf}
+ * @param site The site to get bounding hazards
+ * @param baseGroup The Netcdf base group
+ */
+ public static List<Map<SiteClass, Map<Imt, XySequence>>> boundingHazards(
+ NshmNetcdfReader netcdf,
+ Location site) {
+ return new BoundingHazards(netcdf, site).boundingHazards;
+ }
+ private void setBoundingHazards(Location site) {
var longitudes = coords.locations().stream().mapToDouble(loc -> loc.longitude).toArray();
var latitudes = coords.locations().stream().mapToDouble(loc -> loc.latitude).toArray();
- idxLonLL = NetcdfUtils.getIdxLTEQ(longitudes, site.longitude);
- idxLatLL = NetcdfUtils.getIdxLTEQ(latitudes, site.latitude);
+ var idxLonLL = NetcdfUtils.getIdxLTEQ(longitudes, site.longitude);
+ var idxLatLL = NetcdfUtils.getIdxLTEQ(latitudes, site.latitude);
boundingHazards = extractHazardsAt(idxLonLL, idxLatLL);
@@ -54,20 +65,6 @@ class BoundingHazards {
boundingHazards.add(calcTargetHazards(fracLon, fracLat));
}
- /**
- * Returns the bounding hazards at four closet grid points to target.
- *
- * @param netcdf The {@code Netcdf}
- * @param site The site to get bounding hazards
- * @param baseGroup The Netcdf base group
- */
- static List<Map<SiteClass, Map<Imt, XySequence>>> boundingHazards(
- Netcdf netcdf,
- Location site,
- String baseGroup) {
- return new BoundingHazards(netcdf, site, baseGroup).boundingHazards;
- }
-
private Map<SiteClass, Map<Imt, XySequence>> calcTargetHazards(double fracLon, double fracLat) {
var westTarget = getTargetData(boundingHazards.get(0), boundingHazards.get(1), fracLat);
var eastTarget = getTargetData(boundingHazards.get(3), boundingHazards.get(2), fracLat);
@@ -82,11 +79,10 @@ class BoundingHazards {
* empty slot for the interpolated target hazards
*/
private List<Map<SiteClass, Map<Imt, XySequence>>> extractHazardsAt(int idxLonLL, int idxLatLL) {
-
var boundingHazardMaps = new ArrayList<Map<SiteClass, Map<Imt, XySequence>>>(5);
try (NetcdfDataset ncd = NetcdfDataset.openDataset(netcdf.path().toString())) {
- Group targetGroup = ncd.findGroup(baseGroup);
+ Group targetGroup = ncd.findGroup(netcdf.nshmGroup().toString());
// TODO: rename variable in netCDF
Variable vHazards = targetGroup.findVariable(Key.AEPS);
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/netcdf/NetcdfCoordinates.java b/src/main/java/gov/usgs/earthquake/nshmp/netcdf/reader/NetcdfCoordinates.java
similarity index 67%
rename from src/main/java/gov/usgs/earthquake/nshmp/netcdf/NetcdfCoordinates.java
rename to src/main/java/gov/usgs/earthquake/nshmp/netcdf/reader/NetcdfCoordinates.java
index 43c6d3910479b17840b13dd4fe7ba4eee2fba764..9627d73d4229c5574605704d764c89cd2a32a3ad 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/netcdf/NetcdfCoordinates.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/netcdf/reader/NetcdfCoordinates.java
@@ -1,4 +1,4 @@
-package gov.usgs.earthquake.nshmp.netcdf;
+package gov.usgs.earthquake.nshmp.netcdf.reader;
import static com.google.common.base.Preconditions.checkArgument;
@@ -13,8 +13,11 @@ import com.google.common.collect.Maps;
import gov.usgs.earthquake.nshmp.geo.Location;
import gov.usgs.earthquake.nshmp.geo.LocationList;
+import gov.usgs.earthquake.nshmp.geo.Region;
+import gov.usgs.earthquake.nshmp.geo.Regions;
import gov.usgs.earthquake.nshmp.gmm.Imt;
-import gov.usgs.earthquake.nshmp.netcdf.NetcdfUtils.Key;
+import gov.usgs.earthquake.nshmp.netcdf.SiteClass;
+import gov.usgs.earthquake.nshmp.netcdf.reader.NetcdfUtils.Key;
import ucar.ma2.DataType;
import ucar.ma2.InvalidRangeException;
@@ -22,7 +25,7 @@ import ucar.nc2.Group;
import ucar.nc2.Variable;
/*
- * Container for dimensions and coordinate variables of nshmp netCDF file to
+ * Container for dimensions and coordinate variables of NSHMP NetCDF file to
* facilitate indexing operations prior to data retrieval.
*/
public class NetcdfCoordinates {
@@ -32,23 +35,17 @@ public class NetcdfCoordinates {
private final LocationList locations;
private final Map<SiteClass, Map<Imt, double[]>> imls;
private final int nIml;
+ private final Region region;
- NetcdfCoordinates(Group targetGroup) throws IOException {
+ public NetcdfCoordinates(Group targetGroup) throws IOException {
// This bypasses the netCDF dimensions, but since we know what the
// variables and their dimensions should be, this is OK(???)
- // get coordinate variables
- var vVs30s = targetGroup.findVariable(Key.VS30);
- var vImts = targetGroup.findVariable(Key.IMT);
- var vlats = targetGroup.findVariable(Key.LAT);
- var vlons = targetGroup.findVariable(Key.LON);
var vImls = targetGroup.findVariable(Key.IMLS);
-
- // read coordinate variables into java arrays
- var vs30s = (int[]) vVs30s.read().get1DJavaArray(DataType.INT);
- var imtVals = (double[]) vImts.read().get1DJavaArray(DataType.DOUBLE);
- var lats = (double[]) vlats.read().get1DJavaArray(DataType.DOUBLE);
- var lons = (double[]) vlons.read().get1DJavaArray(DataType.DOUBLE);
+ var vs30s = NetcdfUtils.getIntArray(targetGroup, Key.VS30);
+ var imtVals = NetcdfUtils.getDoubleArray(targetGroup, Key.IMT);
+ var lats = NetcdfUtils.getDoubleArray(targetGroup, Key.LAT);
+ var lons = NetcdfUtils.getDoubleArray(targetGroup, Key.LON);
var builder = LocationList.builder();
for (int i = 0; i < lons.length; i++) {
@@ -56,6 +53,7 @@ public class NetcdfCoordinates {
}
locations = builder.build();
+ region = Regions.createRectangular("Bounds", locations.bounds().min, locations.bounds().max);
// vImls has dimensions (vs30, Imt, Iml)
// alternatively get nIml from Dimension Iml
@@ -76,42 +74,51 @@ public class NetcdfCoordinates {
imls = mapImls(vImls);
}
- LocationList locations() {
+ /**
+ * Returns the locations associated with a {@code NshmGroup}
+ */
+ public LocationList locations() {
return LocationList.copyOf(locations);
}
- int nIml() {
+ /**
+ * Returns the number of Imls associated with a {@code NshmGroup}.
+ */
+ public int nIml() {
return nIml;
}
- List<SiteClass> siteClasses() {
+ /**
+ * Return the site classes associated with a {@code NshmGroup}.
+ */
+ public List<SiteClass> siteClasses() {
return List.copyOf(siteClasses);
}
- List<Imt> imt() {
+ /**
+ * Return the Imts associated with a {@code NshmGroup}.
+ */
+ public List<Imt> imt() {
return List.copyOf(imts);
}
- Map<SiteClass, Map<Imt, double[]>> iml() {
+ /**
+ * Returns the Imls associated with a {@code NshmGroup}.
+ */
+ public Map<SiteClass, Map<Imt, double[]>> iml() {
return imls;
}
- /*
- * validate target coordinates
+ /**
+ * Validate a target site is contained with in the bounds.
+ *
+ * @param site The site to test
*/
- void checkCoords(Location site) {
+ public void contains(Location site) {
var bounds = locations.bounds();
- var minLon = bounds.min.longitude;
- var maxLon = bounds.max.longitude;
- var minLat = bounds.min.latitude;
- var maxLat = bounds.max.latitude;
- var lon = site.longitude;
- var lat = site.latitude;
-
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));
+ region.contains(site),
+ String.format("Target site [%s] out of range %s", site.toString(), bounds.toString()));
}
/*
@@ -123,7 +130,6 @@ public class NetcdfCoordinates {
* hazard curves...
*/
private Map<SiteClass, Map<Imt, double[]>> mapImls(Variable vImls) {
-
EnumMap<SiteClass, Map<Imt, double[]>> vsImtImlMap = Maps.newEnumMap(SiteClass.class);
for (int i = 0; i < siteClasses.size(); i++) {
@@ -138,7 +144,8 @@ public class NetcdfCoordinates {
var shape = new int[] { 1, 1, nIml };
try {
- imtImlMap.put(imt,
+ imtImlMap.put(
+ imt,
(double[]) vImls.read(origin, shape).reduce().get1DJavaArray(DataType.DOUBLE));
} catch (IOException | InvalidRangeException e) {
var msg = "Failed read attempt for vImls with origin: " +
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/netcdf/NetcdfUtils.java b/src/main/java/gov/usgs/earthquake/nshmp/netcdf/reader/NetcdfUtils.java
similarity index 72%
rename from src/main/java/gov/usgs/earthquake/nshmp/netcdf/NetcdfUtils.java
rename to src/main/java/gov/usgs/earthquake/nshmp/netcdf/reader/NetcdfUtils.java
index 28a712c6a78df6240272657a9b8687661eb6fcd6..3e7d1b15ee044c75029db56bd2748de7b7f47004 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/netcdf/NetcdfUtils.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/netcdf/reader/NetcdfUtils.java
@@ -1,5 +1,8 @@
-package gov.usgs.earthquake.nshmp.netcdf;
+package gov.usgs.earthquake.nshmp.netcdf.reader;
+import static com.google.common.base.Preconditions.checkNotNull;
+
+import java.io.IOException;
import java.util.Arrays;
import java.util.Map;
@@ -8,9 +11,52 @@ import com.google.common.math.DoubleMath;
import gov.usgs.earthquake.nshmp.data.XySequence;
import gov.usgs.earthquake.nshmp.gmm.Imt;
+import gov.usgs.earthquake.nshmp.netcdf.SiteClass;
+
+import ucar.ma2.DataType;
+import ucar.nc2.Group;
class NetcdfUtils {
+ /**
+ * Returns a {@code double[]} from a NetCDF group
+ *
+ * @param group The NetCDF group
+ * @param key The key to read from the group
+ * @throws IOException
+ */
+ static double[] getDoubleArray(Group group, String key) throws IOException {
+ return (double[]) get1DArray(group, key, DataType.DOUBLE);
+ }
+
+ /**
+ * Returns a {@code int[]} from a NetCDF group
+ *
+ * @param group The NetCDF group
+ * @param key The key to read from the group
+ * @throws IOException
+ */
+ static int[] getIntArray(Group group, String key) throws IOException {
+ return (int[]) get1DArray(group, key, DataType.INT);
+ }
+
+ /**
+ * Get a 1D array from a NetCDF group.
+ *
+ * @param group The NetCDF group
+ * @param key The key to read from the group
+ * @param dataType The data type to read
+ * @throws IOException
+ */
+ static Object get1DArray(Group group, String key, DataType dataType) throws IOException {
+ var var = group.findVariable(key);
+ checkNotNull(
+ var,
+ String.format("Could not find variable [%s] in group [%s]", key, group.getFullName()));
+
+ return var.read().get1DJavaArray(dataType);
+ }
+
/*
* 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