Merge pull request #238 from pmpowers-usgs/system-rate-237

System rate 237

README.md

@@ -1,6 +1,6 @@
 nshmp-haz
 =========
 
-U.S. Geological Survey (USGS) National Seismic Hazard Model Project (NSHMP) codes.
+U.S. Geological Survey ([USGS](https://www.usgs.gov)) national neismic hazard mapping project ([NSHMP](https://earthquake.usgs.gov/hazards/)) codes for performing probabilistic seismic hazard (PSHA) and related analyses.
 
-Information relevant to obtaining, building, and running the code may be found in the [Wiki](https://github.com/usgs/nshmp-haz/wiki/).
+These codes are intended for use with models developed by the NSHMP. Information relevant to obtaining, building, and running the code may be found in the [wiki](https://github.com/usgs/nshmp-haz/wiki/).

build.xml

@@ -230,7 +230,7 @@
              encoding="UTF-8"
              docencoding="UTF-8"
              charset="UTF-8"
-             additionalparam="-notimestamp">
+             additionalparam="-notimestamp -Xdoclint:none">
       <packageset dir="${src}">
         <include name="org/opensha2/**" />
         <exclude name="org/opensha2/etc/**" />

src/org/opensha2/calc/EqRate.java

@@ -17,6 +17,7 @@
 import org.opensha2.eq.model.SystemSourceSet;
 import org.opensha2.geo.Location;
 import org.opensha2.mfd.Mfds;
+import org.opensha2.util.Maths;
 
 import com.google.common.base.Converter;
 import com.google.common.collect.ImmutableMap;
@@ -28,8 +29,8 @@
 import java.util.concurrent.Callable;
 
 /**
- * General purpose magnitude-frequency distribution (MFD) data container. This
- * class makes no distinction between incremental or cumulative MFDs, or whether
+ * General purpose earthquake rate and probability data container. This class
+ * makes no distinction between incremental or cumulative MFDs, or whether
  * values are stored as annual-rate or poisson probability.
  *
  * @author Peter Powers
@@ -164,7 +165,9 @@ public static EqRate toCumulative(EqRate incremental) {
    *        conversion
    */
   public static EqRate toPoissonProbability(EqRate annualRates, double timespan) {
-    Converter<Double, Double> converter = Mfds.annualRateToProbabilityConverter(timespan);
+    Converter<Double, Double> converter =
+        Mfds.annualRateToProbabilityConverter(timespan)
+            .andThen(Maths.decimalToProbabilityConverter(2));
     XySequence totalMfd = XySequence
         .copyOf(annualRates.totalMfd)
         .transform(converter);
@@ -189,8 +192,8 @@ public static EqRate toPoissonProbability(EqRate annualRates, double timespan) {
    * <p><b>NOTE:</b> This operation is additive and will produce meaningless
    * results if {@code rates} have already been converted to
    * {@link #toPoissonProbability(EqRate, double) probabilities}, or are not all
-   * of {@link DistributionFormat#INCREMENTAL} or {@link DistributionFormat#CUMULATIVE}
-   * distribution format.
+   * of {@link DistributionFormat#INCREMENTAL} or
+   * {@link DistributionFormat#CUMULATIVE} distribution format.
    * 
    * <p>Buyer beware.
    * 

src/org/opensha2/calc/EqRateExport.java

@@ -36,8 +36,12 @@
  */
 public final class EqRateExport {
 
+  private static final String RATE_FORMAT = "%.8g";
+  private static final String PROB_FORMAT = "%.2f";
+
   private final Logger log;
   private final Path dir;
+  private final String valueFormat;
   private final CalcConfig config;
   private final boolean exportSource;
 
@@ -53,8 +57,13 @@ public final class EqRateExport {
   private final List<EqRate> rates;
 
   private EqRateExport(CalcConfig config, Sites sites, Logger log) throws IOException {
+
+    // whether or not rates or probabilities have been calculated
+    boolean rates = config.rate.valueFormat == ValueFormat.ANNUAL_RATE;
+
     this.log = log;
-    this.dir = HazardExport.createOutputDir(improvedOutputDirectory(config));
+    this.dir = HazardExport.createOutputDir(updateOutDir(config.output.directory, rates));
+    this.valueFormat = rates ? RATE_FORMAT : PROB_FORMAT;
     this.config = config;
     this.exportSource = config.output.dataTypes.contains(DataType.SOURCE);
     this.rates = new ArrayList<>();
@@ -66,17 +75,12 @@ private EqRateExport(CalcConfig config, Sites sites, Logger log) throws IOExcept
     this.totalWatch = Stopwatch.createStarted();
   }
 
-  /*
-   * If output from config is 'curves', change to the more appropriate 'eq-rate'
-   * or 'eq-prob'.
-   */
-  static Path improvedOutputDirectory(CalcConfig config) {
-    Path out = config.output.directory;
-    if (out.toString().equals(CalcConfig.DEFAULT_OUT)) {
-      return (config.rate.valueFormat == ValueFormat.POISSON_PROBABILITY) ? Paths.get("eq-prob")
-          : Paths.get("eq-rate");
+  /* If config output is 'curves', change to 'eq-rate' or 'eq-prob'. */
+  static Path updateOutDir(Path dir, boolean rates) {
+    if (dir.toString().equals(CalcConfig.DEFAULT_OUT)) {
+      return (rates ? Paths.get("eq-rate") : Paths.get("eq-prob"));
     }
-    return out;
+    return dir;
   }
 
   /**
@@ -189,7 +193,7 @@ private void writeRates() throws IOException {
 
     OpenOption[] options = firstBatch ? HazardExport.WRITE : HazardExport.APPEND;
 
-    Function<Double, String> formatter = Parsing.formatDoubleFunction(HazardExport.RATE_FMT);
+    Function<Double, String> formatter = Parsing.formatDoubleFunction(valueFormat);
 
     /* Line maps for ascii output; may or may not be used */
     List<String> totalLines = new ArrayList<>();

src/org/opensha2/eq/model/SystemSourceSet.java

@@ -242,7 +242,6 @@ private final double width() {
     private final double rake() {
       return rakes[index];
     }
-
   }
 
   /**
@@ -395,13 +394,13 @@ SystemSourceSet build() {
           stats);
     }
   }
-  
+
   /*
-   * Handle rate calculations internally as SystemSource is not fully implemented.
-   * If/when it is, this should be removed in favor using iterableForLocation
-   * and getRupture(0).
+   * Handle rate calculations internally as SystemSource is not fully
+   * implemented. If/when it is, this should be removed in favor using
+   * iterableForLocation and getRupture(0).
    */
-  
+
   /**
    * Return an instance of a {@code Function} that converts a
    * {@code SystemSourceSet} to a ground motion model {@code InputList}.
@@ -427,7 +426,7 @@ private static final class ToRates implements Function<SystemSourceSet, Interval
         final Location location,
         final double distance,
         final IntervalArray modelMfd) {
-      
+
       this.location = location;
       this.distance = distance;
       this.modelMfd = modelMfd;
@@ -436,19 +435,18 @@ private static final class ToRates implements Function<SystemSourceSet, Interval
     @Override
     public IntervalArray apply(final SystemSourceSet sourceSet) {
       IntervalArray.Builder mfdForLocation = IntervalArray.Builder.fromModel(modelMfd);
-      BitSet bitsetForLocation = sourceSet.bitsetForLocation(location, distance);
-      if (bitsetForLocation.isEmpty()) {
+      BitSet siteBitset = sourceSet.bitsetForLocation(location, distance);
+      if (siteBitset.isEmpty()) {
         return modelMfd;
       }
-      int[] sourceIndices = Indexing.bitsToIndices(bitsetForLocation);
-      for (int i : sourceIndices) {
-        mfdForLocation.add(sourceSet.mags[i], sourceSet.rates[i]);
+      Predicate<SystemSource> distanceFilter = new BitsetFilter(siteBitset);
+      for (SystemSource source : Iterables.filter(sourceSet, distanceFilter)) {
+        mfdForLocation.add(source.magnitude(), source.rate());
       }
       return mfdForLocation.multiply(sourceSet.weight()).build();
     }
   }
 
-
   /*
    * System source calculation pipeline.
    *
@@ -593,23 +591,28 @@ public int compare(double[] left, double[] right) {
     }
   }
 
+  /*
+   * Predicate that tests the intersection of a site bitset (fault sections
+   * wihtin a specified distance of a site) with source bitsets (fault sections
+   * that participate in a SystemSource/Rupture).
+   */
   private static class BitsetFilter implements Predicate<SystemSource> {
 
     private static final String ID = "BitsetFilter";
-    private final BitSet bitset;
+    private final BitSet siteBitset;
 
-    BitsetFilter(BitSet bitset) {
-      this.bitset = bitset;
+    BitsetFilter(BitSet siteBitset) {
+      this.siteBitset = siteBitset;
     }
 
     @Override
     public boolean apply(SystemSource source) {
-      return bitset.intersects(source.bitset());
+      return siteBitset.intersects(source.bitset());
     }
 
     @Override
     public String toString() {
-      return ID + " " + bitset;
+      return ID + " " + siteBitset;
     }
   }
 
@@ -636,13 +639,13 @@ private static final class InputGenerator implements Function<SystemSource, Haza
     public HazardInput apply(SystemSource source) {
 
       /* Find r minima. */
-      BitSet sectionBitset = source.bitset();
+      BitSet sections = source.bitset();
       double rJB = Double.MAX_VALUE;
       double rRup = Double.MAX_VALUE;
       double rX = Double.MAX_VALUE;
       int hitCount = 0;
       for (int sectionIndex : rMap.keySet()) {
-        if (sectionBitset.get(sectionIndex)) {
+        if (sections.get(sectionIndex)) {
           double[] distances = rMap.get(sectionIndex);
           rJB = min(rJB, distances[R_JB_INDEX]);
           double rRupNew = distances[R_RUP_INDEX];

src/org/opensha2/gmm/ZhaoEtAl_2016.java

@@ -27,7 +27,7 @@
  * Abstract implementation of the shallow crustal, upper mantle, subduction
  * interface, and subduction slab ground motion models by Zhao et al. (2016).
  * 
- * <p><b>Implementation notes:</b>
+ * <p><b>Implementation notes:</b><ul>
  * 
  * <li>All models supply site-class specific sigma, however, only the total
  * sigma is used here as reported in the various coefficient tables.</li>

src/org/opensha2/mfd/Mfds.java

@@ -352,15 +352,17 @@ public static double probToRate(double P, double timespan) {
 
   /**
    * Return a converter between annual rate and Poisson probability over a
-   * 1-year time span.
+   * 1-year time span. The converter expects probabilities to be represented as
+   * fractions of 1.0.
    */
   public static Converter<Double, Double> annualRateToProbabilityConverter() {
     return new AnnRateToPoissProbConverter(1.0);
   }
 
   /**
    * Return a converter between annual rate and Poisson probability over the
-   * specified time span.
+   * specified time span. The converter expects probabilities to be represented
+   * as fractions of 1.0.
    */
   public static Converter<Double, Double> annualRateToProbabilityConverter(double timespan) {
     return new AnnRateToPoissProbConverter(timespan);

src/org/opensha2/util/Maths.java

@@ -1,5 +1,7 @@
 package org.opensha2.util;
 
+import com.google.common.base.Converter;
+
 import java.math.BigDecimal;
 import java.math.RoundingMode;
 
@@ -148,4 +150,40 @@ public static double round(double value, int scale, RoundingMode mode) {
     return BigDecimal.valueOf(value).setScale(scale, mode).doubleValue();
   }
 
+  /**
+   * Return a converter between decimal values and percentages. The forward
+   * operation of this converter <i>may</i> be lossy in as much as the supplied
+   * decimal value will be rounded to the specified scale after conversion to a
+   * percentage. For instance:
+   * 
+   * <p>{@code decimalToProbabilityConverter(2).convert(0.23456) = 23.46}
+   * 
+   * <p>Reverse operations do not affect precision at this time.
+   * 
+   * @param percentScale the number of decimal places in percentages output by
+   *        this converter
+   */
+  public static Converter<Double, Double> decimalToProbabilityConverter(int percentScale) {
+    return new DecimalToProbabilityConverter(percentScale);
+  }
+
+  private static class DecimalToProbabilityConverter extends Converter<Double, Double> {
+
+    private final int percentScale;
+
+    DecimalToProbabilityConverter(int percentScale) {
+      this.percentScale = percentScale;
+    }
+
+    @Override
+    protected Double doBackward(Double percent) {
+      return percent / 100.0;
+    }
+
+    @Override
+    protected Double doForward(Double decimal) {
+      return round(decimal * 100.0, percentScale);
+    }
+  }
+
 }