From f62b6cee577e4d61ca58753a1f3149a46e0c1628 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 06:57:09 -0700
Subject: [PATCH 01/16] deleted stale test class
---
.../nshmp/programs/HazardCurveTest.java | 18 ------------------
1 file changed, 18 deletions(-)
delete mode 100644 src/test/java/gov/usgs/earthquake/nshmp/programs/HazardCurveTest.java
diff --git a/src/test/java/gov/usgs/earthquake/nshmp/programs/HazardCurveTest.java b/src/test/java/gov/usgs/earthquake/nshmp/programs/HazardCurveTest.java
deleted file mode 100644
index 8ffeefca0..000000000
--- a/src/test/java/gov/usgs/earthquake/nshmp/programs/HazardCurveTest.java
+++ /dev/null
@@ -1,18 +0,0 @@
-package gov.usgs.earthquake.nshmp.programs;
-
-import org.junit.jupiter.api.BeforeEach;
-import org.junit.jupiter.api.Test;
-
-public class HazardCurveTest {
-
- @BeforeEach
- public void setUpBeforeClass() throws Exception {}
-
- @Test
- public final void testRun() {
- // String[] args = new String[] {};
- // String status = HazardCalc.run(args);
- // assertEquals(HazardCalc.USAGE.substring(0,18), status.substring(0,18));
- }
-
-}
--
GitLab
From 4eaf9b8675c5b7c2808a992f8c102e8e75b65642 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 06:57:27 -0700
Subject: [PATCH 02/16] cleaned up TODOs
---
.../gov/usgs/earthquake/nshmp/DisaggCalc.java | 8 -----
.../gov/usgs/earthquake/nshmp/RateCalc.java | 3 --
.../usgs/earthquake/nshmp/site/NshmpSite.java | 4 ---
.../earthquake/nshmp/site/NshmpSiteFiles.java | 31 ++++++++--------
.../earthquake/nshmp/www/ServletUtil.java | 2 --
.../nshmp/www/hazard/HazardService.java | 7 ++--
.../nshmp/www/services/RateService.java | 5 ++-
.../nshmp/www/services/SourceServices.java | 35 +------------------
8 files changed, 23 insertions(+), 72 deletions(-)
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/DisaggCalc.java b/src/main/java/gov/usgs/earthquake/nshmp/DisaggCalc.java
index de59f18b2..1250ee5b8 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/DisaggCalc.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/DisaggCalc.java
@@ -260,10 +260,6 @@ public class DisaggCalc {
/*
* Compute hazard curves using the supplied model, config, and sites. Method
* returns the path to the directory where results were written.
- *
- * TODO consider refactoring to supply an Optional<Double> return period to
- * HazardCalc.calc() that will trigger disaggregations if the value is
- * present.
*/
private static Path calcRp(
HazardModel model,
@@ -353,10 +349,6 @@ public class DisaggCalc {
/*
* Compute hazard curves using the supplied model, config, and sites. Method
* returns the path to the directory where results were written.
- *
- * TODO consider refactoring to supply an Optional<Double> return period to
- * HazardCalc.calc() that will trigger disaggregations if the value is
- * present.
*/
private static Path calcIml(
HazardModel model,
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/RateCalc.java b/src/main/java/gov/usgs/earthquake/nshmp/RateCalc.java
index 8c59131d9..d2a3fd5c0 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/RateCalc.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/RateCalc.java
@@ -186,9 +186,6 @@ public class RateCalc {
* there are one or more longer-running calcs in the batch, processing
* batches of locations to a List preserves submission order; as opposed to
* using FutureCallbacks, which will reorder sites on export.
- *
- * TODO this is a terrible implementation with batch size 10. resulted from
- * refactor to exports not queueing results
*/
for (Site site : sites) {
Callable<EqRate> task = EqRate.callable(model, config, site);
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/site/NshmpSite.java b/src/main/java/gov/usgs/earthquake/nshmp/site/NshmpSite.java
index f8754e839..21ef1cd42 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/site/NshmpSite.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/site/NshmpSite.java
@@ -20,10 +20,6 @@ import gov.usgs.earthquake.nshmp.internal.UsRegion;
*/
public enum NshmpSite implements NamedLocation {
- // TODO move this and other nshmp specific classes to nshmp-haz
- // TODO update output files which should also be part of nshmp-haz
- // TODO do we need ATC sites?
-
/* Northern CA (16) */
BIG_SUR_CA(-121.75, 36.25),
COALINGA_CA(-120.40, 36.15),
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/site/NshmpSiteFiles.java b/src/main/java/gov/usgs/earthquake/nshmp/site/NshmpSiteFiles.java
index 5d1022116..cb633b94f 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/site/NshmpSiteFiles.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/site/NshmpSiteFiles.java
@@ -56,7 +56,7 @@ import gov.usgs.earthquake.nshmp.geo.json.Properties.Style;
*/
final class NshmpSiteFiles {
- // TODO consider removing this to nshm-model-dev
+ // Consider removing this to nshm-model-dev
// keeping the outputs in nshmp-haz
/*
@@ -185,19 +185,24 @@ final class NshmpSiteFiles {
static void writeNshmpSummaryPoly() throws IOException {
Set<NshmpPolygon> polys = EnumSet.range(LA_BASIN, UCERF3_NSHM14);
+
+ List<String> nameList = polys.stream()
+ .map(Functions.toStringFunction())
+ .collect(Collectors.toList());
+
+ List<LocationList> coordList = polys.stream()
+ .map(new Function<NshmpPolygon, LocationList>() {
+ @Override
+ public LocationList apply(NshmpPolygon poly) {
+ return poly.coordinates();
+ }
+ }::apply)
+ .collect(Collectors.toList());
+
writePolysJson(
EXPORT_DIR.resolve("map-nshmp-all.geojson"),
- polys.stream()
- .map(Functions.toStringFunction())
- .collect(Collectors.toList()),
- polys.stream()
- .map(new Function<NshmpPolygon, LocationList>() {
- @Override
- public LocationList apply(NshmpPolygon poly) {
- return poly.coordinates();
- }
- }::apply)
- .collect(Collectors.toList()));
+ nameList,
+ coordList);
}
static void writePolysJson(
@@ -210,7 +215,6 @@ final class NshmpSiteFiles {
.put("spacing", 0.1);
int i = 0;
- // TODO this incrementer is messed up
// can't name and coords come as a map?
for (LocationList border : coordList) {
props.put(Style.TITLE, nameList.get(i++));
@@ -395,7 +399,6 @@ final class NshmpSiteFiles {
.put(Style.MARKER_SIZE, "small");
for (NamedLocation loc : sites) {
- // TODO test loc vs loc.toString()
b.add(Feature.point(loc.location())
.properties(props
.put(Style.TITLE, loc.toString())
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/www/ServletUtil.java b/src/main/java/gov/usgs/earthquake/nshmp/www/ServletUtil.java
index 3e3b7425d..ec22fe0c2 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/www/ServletUtil.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/www/ServletUtil.java
@@ -32,7 +32,6 @@ import gov.usgs.earthquake.nshmp.calc.ValueFormat;
import gov.usgs.earthquake.nshmp.gmm.Imt;
import gov.usgs.earthquake.nshmp.model.HazardModel;
import gov.usgs.earthquake.nshmp.www.meta.MetaUtil;
-
import io.micronaut.context.annotation.Value;
import io.micronaut.context.event.ShutdownEvent;
import io.micronaut.context.event.StartupEvent;
@@ -64,7 +63,6 @@ public class ServletUtil {
private static HazardModel HAZARD_MODEL;
static {
- /* TODO modified for disagg-epsilon branch; should be context var */
THREAD_COUNT = getRuntime().availableProcessors();
CALC_EXECUTOR = MoreExecutors.listeningDecorator(Executors.newFixedThreadPool(THREAD_COUNT));
TASK_EXECUTOR = Executors.newSingleThreadExecutor();
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/www/hazard/HazardService.java b/src/main/java/gov/usgs/earthquake/nshmp/www/hazard/HazardService.java
index c5c278ee2..41641e3be 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/www/hazard/HazardService.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/www/hazard/HazardService.java
@@ -39,7 +39,6 @@ import gov.usgs.earthquake.nshmp.www.ServletUtil;
import gov.usgs.earthquake.nshmp.www.meta.DoubleParameter;
import gov.usgs.earthquake.nshmp.www.meta.Parameter;
import gov.usgs.earthquake.nshmp.www.services.SourceServices.SourceModel;
-
import io.micronaut.http.HttpRequest;
import io.micronaut.http.HttpResponse;
import jakarta.inject.Singleton;
@@ -162,7 +161,7 @@ public final class HazardService {
Metadata(HazardModel model) {
this.model = new SourceModel(model);
- // TODO need min max from model
+ // should get min max from model
longitude = new DoubleParameter(
"Longitude",
"°",
@@ -252,7 +251,7 @@ public final class HazardService {
}
Builder hazard(Hazard hazard) {
- // TODO necessary??
+ // necessary??
checkState(totalMap == null, "Hazard has already been added to this builder");
componentMaps = new EnumMap<>(Imt.class);
@@ -347,7 +346,7 @@ public final class HazardService {
* If entire curve is <1e-4, this method will return a curve consisting of
* just the first point in the supplied curve.
*
- * TODO We probably want to move the TRUNCATION_LIMIT out to a config.
+ * Consider moving to config.
*/
double[] yValues = curve.yValues().toArray();
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/www/services/RateService.java b/src/main/java/gov/usgs/earthquake/nshmp/www/services/RateService.java
index d4b81df81..500167ba5 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/www/services/RateService.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/www/services/RateService.java
@@ -27,7 +27,6 @@ import gov.usgs.earthquake.nshmp.www.ServletUtil;
import gov.usgs.earthquake.nshmp.www.WsUtils;
import gov.usgs.earthquake.nshmp.www.meta.DoubleParameter;
import gov.usgs.earthquake.nshmp.www.meta.Metadata.DefaultParameters;
-
import io.micronaut.http.HttpRequest;
import io.micronaut.http.HttpResponse;
import jakarta.inject.Singleton;
@@ -311,8 +310,8 @@ public final class RateService {
}
/*
- * TODO would rather use this a general container for mfds and hazard curves.
- * See HazardService.Curve
+ * Would rather use this a general container for mfds and hazard curves. See
+ * HazardService.Curve
*/
private static class Sequence {
final String component;
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/www/services/SourceServices.java b/src/main/java/gov/usgs/earthquake/nshmp/www/services/SourceServices.java
index b473fd92f..bb6cbd904 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/www/services/SourceServices.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/www/services/SourceServices.java
@@ -21,7 +21,6 @@ import gov.usgs.earthquake.nshmp.www.ResponseBody;
import gov.usgs.earthquake.nshmp.www.ServletUtil;
import gov.usgs.earthquake.nshmp.www.WsUtils;
import gov.usgs.earthquake.nshmp.www.meta.Parameter;
-
import io.micronaut.http.HttpRequest;
import io.micronaut.http.HttpResponse;
import jakarta.inject.Singleton;
@@ -70,47 +69,21 @@ public class SourceServices {
}
/*
- * TODO service metadata should be in same package as services (why
+ * task... service metadata should be in same package as services (why
* ResponseData is currently public); rename meta package to
*/
public static class ResponseData {
final String description;
final Object server;
- // final Parameters parameters;
public ResponseData() {
this.description = "Installed source model listing";
this.server = ServletUtil.serverData(
ServletUtil.THREAD_COUNT,
Stopwatch.createStarted());
- // this.parameters = new Parameters();
}
}
- // static class Parameters {
- // List<SourceModel> models;
- // DoubleParameter returnPeriod;
- // DoubleParameter vs30;
- //
- // Parameters() {
- // models = ServletUtil.hazardModels().stream()
- // .map(SourceModel::new)
- // .collect(Collectors.toList());
- //
- // returnPeriod = new DoubleParameter(
- // "Return period",
- // "years",
- // 100.0,
- // 1e6);
- //
- // vs30 = new DoubleParameter(
- // "Vs30",
- // "m/s",
- // 150,
- // 1500);
- // }
- // }
-
public static class SourceModel {
String name;
Set<Gmm> gmms;
@@ -129,12 +102,6 @@ public class SourceServices {
.map(imt -> new Parameter(ServletUtil.imtShortLabel(imt), imt.name()))
.collect(toList());
}
-
- // public static List<SourceModel> getList() {
- // return ServletUtil.hazardModels().stream()
- // .map(SourceModel::new)
- // .collect(Collectors.toList());
- // }
}
enum Attributes {
--
GitLab
From 3d9d8198d1df36d0310f4aa699b4b384f02f7c80 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 07:07:39 -0700
Subject: [PATCH 03/16] spotless edits
---
src/main/java/gov/usgs/earthquake/nshmp/www/ServletUtil.java | 1 +
.../java/gov/usgs/earthquake/nshmp/www/hazard/HazardService.java | 1 +
.../java/gov/usgs/earthquake/nshmp/www/services/RateService.java | 1 +
.../gov/usgs/earthquake/nshmp/www/services/SourceServices.java | 1 +
4 files changed, 4 insertions(+)
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/www/ServletUtil.java b/src/main/java/gov/usgs/earthquake/nshmp/www/ServletUtil.java
index ec22fe0c2..49392833d 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/www/ServletUtil.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/www/ServletUtil.java
@@ -32,6 +32,7 @@ import gov.usgs.earthquake.nshmp.calc.ValueFormat;
import gov.usgs.earthquake.nshmp.gmm.Imt;
import gov.usgs.earthquake.nshmp.model.HazardModel;
import gov.usgs.earthquake.nshmp.www.meta.MetaUtil;
+
import io.micronaut.context.annotation.Value;
import io.micronaut.context.event.ShutdownEvent;
import io.micronaut.context.event.StartupEvent;
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/www/hazard/HazardService.java b/src/main/java/gov/usgs/earthquake/nshmp/www/hazard/HazardService.java
index 41641e3be..5f767a08d 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/www/hazard/HazardService.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/www/hazard/HazardService.java
@@ -39,6 +39,7 @@ import gov.usgs.earthquake.nshmp.www.ServletUtil;
import gov.usgs.earthquake.nshmp.www.meta.DoubleParameter;
import gov.usgs.earthquake.nshmp.www.meta.Parameter;
import gov.usgs.earthquake.nshmp.www.services.SourceServices.SourceModel;
+
import io.micronaut.http.HttpRequest;
import io.micronaut.http.HttpResponse;
import jakarta.inject.Singleton;
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/www/services/RateService.java b/src/main/java/gov/usgs/earthquake/nshmp/www/services/RateService.java
index 500167ba5..8cf9684d7 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/www/services/RateService.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/www/services/RateService.java
@@ -27,6 +27,7 @@ import gov.usgs.earthquake.nshmp.www.ServletUtil;
import gov.usgs.earthquake.nshmp.www.WsUtils;
import gov.usgs.earthquake.nshmp.www.meta.DoubleParameter;
import gov.usgs.earthquake.nshmp.www.meta.Metadata.DefaultParameters;
+
import io.micronaut.http.HttpRequest;
import io.micronaut.http.HttpResponse;
import jakarta.inject.Singleton;
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/www/services/SourceServices.java b/src/main/java/gov/usgs/earthquake/nshmp/www/services/SourceServices.java
index bb6cbd904..03704247e 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/www/services/SourceServices.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/www/services/SourceServices.java
@@ -21,6 +21,7 @@ import gov.usgs.earthquake.nshmp.www.ResponseBody;
import gov.usgs.earthquake.nshmp.www.ServletUtil;
import gov.usgs.earthquake.nshmp.www.WsUtils;
import gov.usgs.earthquake.nshmp.www.meta.Parameter;
+
import io.micronaut.http.HttpRequest;
import io.micronaut.http.HttpResponse;
import jakarta.inject.Singleton;
--
GitLab
From 8c577e1ef9652cffbe682707ca8b781e11558a28 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 07:31:36 -0700
Subject: [PATCH 04/16] doc and comment cleanup
---
.../java/gov/usgs/earthquake/nshmp/HazardMaps.java | 8 +++++---
.../usgs/earthquake/nshmp/site/CybershakeSite.java | 3 ---
.../usgs/earthquake/nshmp/site/NshmpSiteFiles.java | 2 +-
.../gov/usgs/earthquake/nshmp/www/meta/Metadata.java | 12 ------------
.../earthquake/nshmp/www/services/RateService.java | 2 --
5 files changed, 6 insertions(+), 21 deletions(-)
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/HazardMaps.java b/src/main/java/gov/usgs/earthquake/nshmp/HazardMaps.java
index 74cca8223..976bebc16 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/HazardMaps.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/HazardMaps.java
@@ -53,9 +53,11 @@ public class HazardMaps {
*/
public static void main(String[] args) {
if (args.length < 1) {
- System.out.println("Usage: Supply a path to a file of hazard curve results and");
- System.out.println(" optionally a space separated list of return periods (in yr)");
- System.out.println(" default return periods: 475 975 2475");
+ System.out.println("Usage: Supply a path to a file of or directory containing hazard");
+ System.out.println(" curve results and optionally a space separated list of return");
+ System.out.println(" periods (in yr). If a directory is specified, nested curve");
+ System.out.println(" files are expected to be named 'curves.csv'.");
+ System.out.println(" Default return periods: 475 975 2475");
return;
}
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/site/CybershakeSite.java b/src/main/java/gov/usgs/earthquake/nshmp/site/CybershakeSite.java
index 712fb6fc6..381332a46 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/site/CybershakeSite.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/site/CybershakeSite.java
@@ -17,9 +17,6 @@ public enum CybershakeSite implements NamedLocation {
* that there are scattered inconsistencies between the Wills and CVM vs30
* values (e.g. LAPD) Sites beginning with lowercase s have been capitalized.
*
- * CVM vs30 values for [S603, S684], [S474, S476], [S644, S646], and [S688,
- * S689] are identical; waiting on reponse from Callahan or Milner.
- *
* Site S603 is repeated (and commented out) in Inland Empire group.
*/
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/site/NshmpSiteFiles.java b/src/main/java/gov/usgs/earthquake/nshmp/site/NshmpSiteFiles.java
index cb633b94f..07badfde4 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/site/NshmpSiteFiles.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/site/NshmpSiteFiles.java
@@ -82,7 +82,7 @@ final class NshmpSiteFiles {
/*
* Currently, we're exporting map regions as polygons. Although the GeoJSON
- * spec supports polygons with holes (and hence 3-dimensional arrays, we only
+ * spec supports polygons with holes (and hence 3-dimensional arrays), we only
* support singular polygons. Polygons render better than PointStrings in any
* event.
*/
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/www/meta/Metadata.java b/src/main/java/gov/usgs/earthquake/nshmp/www/meta/Metadata.java
index 84227bdce..0f2d40b1d 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/www/meta/Metadata.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/www/meta/Metadata.java
@@ -35,23 +35,11 @@ public final class Metadata {
public static class DefaultParameters {
- // final EnumParameter<Edition> edition;
- // final EnumParameter<Region> region;
final DoubleParameter longitude;
final DoubleParameter latitude;
public DefaultParameters() {
- // edition = new EnumParameter<>(
- // "Model edition",
- // ParamType.STRING,
- // EnumSet.allOf(Edition.class));
- //
- // region = new EnumParameter<>(
- // "Model region",
- // ParamType.STRING,
- // EnumSet.allOf(Region.class));
-
longitude = new DoubleParameter(
"Longitude",
"°",
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/www/services/RateService.java b/src/main/java/gov/usgs/earthquake/nshmp/www/services/RateService.java
index 8cf9684d7..c0bcb47fd 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/www/services/RateService.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/www/services/RateService.java
@@ -139,11 +139,9 @@ public final class RateService {
* probability service has been called.
*/
- // for (var model : ServletUtil.hazardModels()) {
var model = ServletUtil.model();
var rate = process(service, model, site, data.distance, data.timespan);
futureRates.add(rate);
- // }
var rates = futureRates.stream()
.map((future) -> {
--
GitLab
From 80388922a03280a0783d0366dcef4eb4a6057d53 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 08:04:06 -0700
Subject: [PATCH 05/16] removed stale python scripts
---
etc/python/README.md | 11 -----
etc/python/gmm-inputs.csv | 38 ---------------
etc/python/gmmBatchExample.py | 90 -----------------------------------
etc/python/gmmExample.py | 78 ------------------------------
4 files changed, 217 deletions(-)
delete mode 100644 etc/python/README.md
delete mode 100644 etc/python/gmm-inputs.csv
delete mode 100644 etc/python/gmmBatchExample.py
delete mode 100644 etc/python/gmmExample.py
diff --git a/etc/python/README.md b/etc/python/README.md
deleted file mode 100644
index 4fb2e5dd2..000000000
--- a/etc/python/README.md
+++ /dev/null
@@ -1,11 +0,0 @@
-# Using nshmp-haz with Python
-
-There are a few different packages that will allow you to call Java code from Python.
-This example uses jpype. It also uses NumPy to simplify working with the arrays
-returned by the ground motion model calculators.
-
-## Requirements
-
-1. A [build](https://github.com/usgs/nshmp-haz/wiki/building-&-running) of nshmp-haz.
-2. [jpype](http://jpype.readthedocs.io/en/latest/install.html)
-3. [NumPy](http://www.numpy.org/)
diff --git a/etc/python/gmm-inputs.csv b/etc/python/gmm-inputs.csv
deleted file mode 100644
index dc4f5e207..000000000
--- a/etc/python/gmm-inputs.csv
+++ /dev/null
@@ -1,38 +0,0 @@
- dip,
-0,
-2.5,
-5,
-7.5,
-10,
-12.5,
-15,
-17.5,
-20,
-22.5,
-25,
-27.5,
-30,
-32.5,
-35,
-37.5,
-40,
-42.5,
-45,
-47.5,
-50,
-52.5,
-55,
-57.5,
-60,
-62.5,
-65,
-67.5,
-70,
-72.5,
-75,
-77.5,
-80,
-82.5,
-85,
-87.5,
-90,
\ No newline at end of file
diff --git a/etc/python/gmmBatchExample.py b/etc/python/gmmBatchExample.py
deleted file mode 100644
index ff5c3dd4d..000000000
--- a/etc/python/gmmBatchExample.py
+++ /dev/null
@@ -1,90 +0,0 @@
-## nshmp-haz Ground Motion Model (GMM) batch processing example script
-
-import requests
-
-## Read CSV file of GMM inputs
-#
-# Each column of the CSV file is a GMM input parameter with the
-# first row dictating that GMM input field.
-#
-# Example CSV to change only dip:
-# dip,
-# 0.0,
-# 45.0,
-# 90.0,
-#
-# For a full list of GMM input paramters see:
-# http://usgs.github.io/nshmp-haz/javadoc/gov/usgs/earthquake/nshmp/gmm/GmmInput.html
-#
-# If 'null' is supplied as a value or a GMM input field and values are
-# not given, the default values are used:
-# http://usgs.github.io/nshmp-haz/javadoc/gov/usgs/earthquake/nshmp/gmm/GmmInput.Builder.html#withDefaults--
-file = open('gmm-inputs.csv', 'r')
-
-inputs = file.read()
-
-file.close()
-
-
-## URL to POST the CSV file of GMM inputs
-#
-# Must update the URL host if not on localhost.
-#
-# The GMMs must be specified in the URL query string.
-#
-# All GMM services are available to call for batch processing.
-host = 'http://localhost:8080'
-
-service = '/nshmp-haz/gmm/spectra'
-
-url = host + service
-
-query = { 'gmm': [ 'AB_06_PRIME', 'CAMPBELL_03', 'FRANKEL_96' ] }
-
-
-## Conduct HTTP POST Request
-#
-# Conduct a HTTP POST request, sending the CSV file of GMM inputs.
-#
-# The POST response is loaded into a object
-# following the returned JSON structure.
-svcResponse = requests.post(url, data = inputs, params = query).json()
-
-
-## Check Response
-#
-# Check to see if the response returned an error and check
-# to see if the field 'response' exists in the object.
-#
-# If the URL does not contain a query string of GMMs the response
-# returned will be the service usage.
-if svcResponse['status'] == 'error' and ~hasattr(svcResponse, 'response'):
- exit()
-
-
-## Retreive the data
-#
-# Loop through each response spectrum response and obtain the means
-# and sigmas.
-for response in svcResponse['response']:
-
- # Request structure contains the GMMs and GMM input parameters used
- request = response['request']
-
- # The GMMs used for the calculation
- gmms = request['gmms']
-
- # The GMM input parameters used for the calculation
- gmmInput = request['input']
-
- # Get the means
- for means in response['means']['data']:
- data = means['data']
- xMeans = data['xs']
- yMeans = data['ys']
-
- # Get the sigmas
- for sigmas in response['sigmas']['data']:
- data = sigmas['data']
- xSigmas = data['xs']
- ySigmas = data['ys']
diff --git a/etc/python/gmmExample.py b/etc/python/gmmExample.py
deleted file mode 100644
index 5819560c2..000000000
--- a/etc/python/gmmExample.py
+++ /dev/null
@@ -1,78 +0,0 @@
-#!/usr/bin/env python
-## nshmp-haz Ground Motion Model (GMM) calculator example script
-
-# =========================================================================
-# This script provides instruction on how to access ground motion models
-# (GMMs) implemented in the nshmp-haz library.
-# =========================================================================
-
-from jpype import *
-import numpy as np
-
-# Specify path to nshmp-haz library:
-classpath = '/path/to/repository/nshmp-haz-master/build/libs/nshmp-haz.jar'
-
-# Start Java Virtual Machine and add nshmp-haz to classpath:
-startJVM(getDefaultJVMPath(), "-ea",
- "-Djava.class.path={0}".format(classpath))
-
-# Import packages:
-nshmp = JPackage("gov").usgs.earthquake.nshmp.etc
-
-# =========================================================================
-# Single ground motion calcuation:
-
-# Initialize calculator:
-hazMat = nshmp.HazMat.init(classpath)
-
-# Note that hazMat is stateless and reusable and should therefore be
-# initialized only once in a script if doing many calculations.
-
-# Set up a GMM input parameter object. These data are a source and site
-# parameterization that will satisfy all currently implemented Gmms. Note
-# that not all models will necessarily use all parameters.
-gmmparams = nshmp.GmmParams()
-gmmparams.Mw = 6.5
-gmmparams.rJB = 5.0
-gmmparams.rRup = 5.1
-gmmparams.rX = 5.1
-gmmparams.dip = 90.0
-gmmparams.width = 10.0
-gmmparams.zTop = 1.0
-gmmparams.zHyp = 6.0
-gmmparams.rake = 0.0
-gmmparams.vs30 = 760.
-gmmparams.vsInf = True
-gmmparams.z2p5 = np.nan
-gmmparams.z1p0 = np.nan
-
-# Specify a ground motion model. GMM identifiers:
-# http://usgs.github.io/nshmp-haz/javadoc/gov/usgs/earthquake/nshmp/gmm/Gmm.html
-gmm = 'ASK_14';
-
-# Specify an intensity measure type (IMT). IMT identifiers:
-# http://usgs.github.io/nshmp-haz/javadoc/gov/usgs/earthquake/nshmp/gmm/Imt.html
-imt = 'PGA';
-
-# Do a calculation. The MatUtil.calc(gmm, imt, gmmInput) method returns an
-# array of [ln(median ground motion), sigma]
-ln_med_gm, sigma = hazMat.gmmMean(gmm, imt, gmmparams)
-
-print('ln(median ground motion), sigma:')
-print(ln_med_gm, sigma)
-
-# =========================================================================
-# Determinisitic response spectrum calculation:
-
-# The object returned by the MatUtil.spectrum(gmm, gmmInput) method may
-# be converted to NumPy arrays.
-# The returned HazMat Spectrum object is not iterable, so do this array
-# by array.
-spectrumResult = hazMat.gmmSpectrum(gmm, gmmparams)
-pds = np.array(spectrumResult.periods)
-means = np.array(spectrumResult.means)
-sigmas = np.array(spectrumResult.sigmas)
-print('period, mean, sigma:')
-for i in range(len(pds)):
- print(pds[i], means[i], sigmas[i])
-# =========================================================================
--
GitLab
From 7836bcf38c5047fbd4386faac96a4845d5fd4901 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 08:04:20 -0700
Subject: [PATCH 06/16] doc edits
---
etc/examples/README.md | 2 +-
etc/matlab/README.md | 16 +++-------------
2 files changed, 4 insertions(+), 14 deletions(-)
diff --git a/etc/examples/README.md b/etc/examples/README.md
index b557f3baa..343bc5b7f 100644
--- a/etc/examples/README.md
+++ b/etc/examples/README.md
@@ -1,6 +1,6 @@
# Examples
-These examples are designed to be executed locally while following the READMEs on GitHub.
+These examples are designed to be executed locally while following the READMEs on GitLub.
All examples avoid a lengthy call to Java and the `HazardCalc` program by using the following
system alias:
diff --git a/etc/matlab/README.md b/etc/matlab/README.md
index 1c512892c..e6ae912c9 100644
--- a/etc/matlab/README.md
+++ b/etc/matlab/README.md
@@ -1,15 +1,5 @@
# Using nshmp-haz with Matlab
-This is out of date.
-
->**NOTE:** *nshmp-haz* was recently upgraded to Java 8, which supercedes and is
-incompatable with the Java 7 JVM that ships with Matlab. Users will need to set the
-`MATLAB_JAVA` environment variable to point to a Java 8 runtime.
-
-All recent versions of Matlab include a Java runtime environment and it is therefore
-relatively straightforward to use the nshmp-haz library.
-
-## Requirements
-
-1. Matlab R2013B or higher (nshmp-haz targets Java 7; prior versions of Matlab use Java 6).
-2. A [build](https://github.com/usgs/nshmp-haz/wiki/building-&-running) of nshmp-haz.
+The best way to use _nshmp-haz_ with matlab is as a web service. The scripts in this directory
+provide examples of how to access web services for ground motion models (GMMs) that are based
+on the code in this repository.
--
GitLab
From 1beb324324e567637007d4e57da8c77e73e54e5d Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 08:11:05 -0700
Subject: [PATCH 07/16] removed link; most users will read docs on gitlab
---
docs/README.md | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/docs/README.md b/docs/README.md
index a25b0ab48..8b2bfaf03 100644
--- a/docs/README.md
+++ b/docs/README.md
@@ -18,8 +18,7 @@ use *nshmp-haz* as well as underlying model implementation details.
* [Developer Basics](./pages/Developer-Basics.md)
* [Calculation Configuration](./pages/Calculation-Configuration.md)
* [Site Specification](./pages/Site-Specification.md)
- * [Examples](../../etc/examples) (or
- [on GitLab](https://code.usgs.gov/ghsc/nshmp/nshmp-haz/-/tree/main/etc/examples))
+ * [Examples](../../etc/examples)
* [Hazard Model](./pages/Hazard-Model.md)
* [Model Structure](./pages/Model-Structure.md)
* [Model Files](./pages/Model-Files.md)
--
GitLab
From 64050380dd1d8991eb05149c083b9f789874a369 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 08:56:08 -0700
Subject: [PATCH 08/16] updated links in examples
---
etc/examples/1-hazard-curve/README.md | 19 +++++++++++--------
etc/examples/2-custom-config/README.md | 4 ++--
etc/examples/3-sites-file/README.md | 6 +++---
etc/examples/5-complex-model/README.md | 2 +-
etc/examples/6-enhanced-output/README.md | 11 ++++++-----
5 files changed, 23 insertions(+), 19 deletions(-)
diff --git a/etc/examples/1-hazard-curve/README.md b/etc/examples/1-hazard-curve/README.md
index 6891e5968..f136d550c 100644
--- a/etc/examples/1-hazard-curve/README.md
+++ b/etc/examples/1-hazard-curve/README.md
@@ -5,7 +5,7 @@ __Working directory:__ `/path/to/nshmp-haz/etc/examples/1-hazard-curve`
On the command line, navigate to the directory above and execute the following:
```Shell
-hazard ../../peer/models/Set1-Case1 "Test Site, -122.0, 38.0"
+hazard ../../peer/models/Set1-Case1 site.csv
```
The PEER models, such as that designated above, consist of simple cases for different source
@@ -15,28 +15,31 @@ testing. See the [PEER directory](../../peer/) for more information.
The result of this calculation should be available as a single comma-delimited file containing
several total mean hazard curves for PGA in a newly created `hazout` directory. In this example,
the calculation configuration was derived from the model directory and the site is defined in
-file `site.csv`. See the [site specification](https://github.com/usgs/nshmp-haz/wiki/sites)
+file `site.csv`. See the [site specification](../../../docs/pages/Site-Specification.md)
page for more details.
-Note that not all [calculation configuration](https://github.com/usgs/nshmp-haz/wiki/Configuration)
+Note that not all [calculation configuration](../../../docs/pages/Calculation-Configuration.md)
parameters need be supplied; see the [configuration file](../../peer/models/Set1-Case1/config.json)
for this example model.
Also note that all output is written to a `hazout` directory by default, but the output destination
can be specified via the
-[`output.directory`](https://github.com/usgs/nshmp-haz/wiki/configuration#config-output) parameter.
-In addition to hazard curves, the calculation configuration and a log of the calculation
-are also saved.
+[`output.directory`](../../../docs/pages/Calculation-Configuration.md#calculation-configuration-parameters)
+parameter. In addition to hazard curves, the calculation configuration and a log of the calculation
+are also saved. The primary outputs are hazard curves, hazard curves truncated below about 10â»â´,
+and ground motion values derived from the curves for specific return periods.
__Results directory structure:__
```text
1-hazard-curve/
└─ hazout/
- ├─ config.json
+ ├─ calc-config.json
├─ HazardCalc.log
└─ PGA/
- └─ curves.csv
+ ├─ curves.csv
+ ├─ curves-truncated.csv
+ └─ map.csv
```
In the next example, we'll override the model supplied configuration with a custom file.
diff --git a/etc/examples/2-custom-config/README.md b/etc/examples/2-custom-config/README.md
index ca5163209..b0ddba75a 100644
--- a/etc/examples/2-custom-config/README.md
+++ b/etc/examples/2-custom-config/README.md
@@ -13,12 +13,12 @@ In this example we've overridden the configuration supplied by the model. Specif
* The upper end of each hazard curve has been truncated at 3 standard deviations.
* Hazard curves have been saved as poisson probability instead of annual rate.
* Hazard curves have been calculated for 3 `imts`
- ([intensity measures](http://usgs.github.io/nshmp-haz/javadoc/index.html?gov/usgs/earthquake/nshmp/gmm/Imt.html),
+ ([intensity measures](https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/gmm/Imt.html),
or spectral periods).
* The `imls` (intensity measure levels or x-values) of the resultant curves
have been explicitely defined for each `imt`.
-See the [configuration specification](https://github.com/usgs/nshmp-haz/wiki/configuration)
+See the [configuration specification]../../../docs/pages/Calculation-Configuration.md)
for details on default values and supported options and formats.
__Results directory structure:__
diff --git a/etc/examples/3-sites-file/README.md b/etc/examples/3-sites-file/README.md
index 65aa2ba68..2db9bb997 100644
--- a/etc/examples/3-sites-file/README.md
+++ b/etc/examples/3-sites-file/README.md
@@ -6,7 +6,7 @@ To compute hazard at more than one site, one may supply a comma-delimited (\*.cs
or [GeoJSON](http://geojson.org) (\*.geojson) formatted site data file instead:
```Shell
-hazard ../../peer/models/Set1-Case1 sites.csv config.json
+hazard ../../peer/models/Set1-Case1 sites.csv config.json
```
or
@@ -15,8 +15,8 @@ or
hazard ../../peer/models/Set1-Case1 sites.geojson config.json
```
-The [site specification](https://github.com/usgs/nshmp-haz/wiki/sites)
-wiki page provides details on the two file formats. Note that with either format,
+The [site specification](../../../docs/pages/Site-Specification.md)
+page provides details on the two file formats. Note that with either format,
if the name of a site is supplied, it will be included in the first column of any output curve files.
__Results directory structure:__
diff --git a/etc/examples/5-complex-model/README.md b/etc/examples/5-complex-model/README.md
index 156169846..f6fc8b2fc 100644
--- a/etc/examples/5-complex-model/README.md
+++ b/etc/examples/5-complex-model/README.md
@@ -39,7 +39,7 @@ hazard ../../../../nshm-conus map.geojson config-map.json
```
This computes 121 curves over a 2° by 2° area and will give you a sense of how long a larger map
-might take. This small coarse map may take 10 minutes to complete. Note that in the above two
+might take. This small, coarse map may take 10 minutes to complete. Note that in the above two
examples we specified different output directories in the config files for each calculation.
__Results directory structure:__
diff --git a/etc/examples/6-enhanced-output/README.md b/etc/examples/6-enhanced-output/README.md
index efed49718..4283327e0 100644
--- a/etc/examples/6-enhanced-output/README.md
+++ b/etc/examples/6-enhanced-output/README.md
@@ -15,14 +15,15 @@ The config file for this example, `config.json`, specified `GMM` and `SOURCE` as
[output data types][output_types]. Note that the output curves directory now contains additional
directories of curves by source type and GMM.
-[output_types]: ../../../docs/pages/Calculation-Configuration.md#calculation-configuration
+[output_types]: ../../../docs/pages/Calculation-Configuration.md#calculation-configuration-parameters
-See the `nshmp-haz` wiki and javadocs for more information on source types ([Wiki][source_wiki],
-[JavaDoc][source_javadoc]) and GMMs ([Wiki][gmm_wiki], [JavaDoc][gmm_javadoc]).
+See the `nshmp-haz` documentation and javadocs for more information on source types
+([docs][source_docs], [JavaDoc][source_javadoc]) and GMMs
+([docs][gmm_docs], [JavaDoc][gmm_javadoc]).
-[source_wiki]: ../../../docs/pages/Source-Types.md
+[source_docs]: ../../../docs/pages/Source-Types.md
[source_javadoc]: https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/model/SourceType.html
-[gmm_wiki]: ./../../docs/pages/Ground-Motion-Models.md
+[gmm_docs]: ./../../docs/pages/Ground-Motion-Models.md
[gmm_javadoc]: https://earthquake.usgs.gov/nshmp/docs/nshmp-lib/gov/usgs/earthquake/nshmp/gmm/package-summary.html
__Results directory structure:__
--
GitLab
From e4ed979fb2780296d1075d4d015fd46088155276 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 10:08:49 -0700
Subject: [PATCH 09/16] readme edits
---
etc/examples/2-custom-config/README.md | 16 +++++++++++-----
etc/examples/3-sites-file/README.md | 12 +++++++++---
.../gov/usgs/earthquake/nshmp/HazardMaps.java | 6 +++---
3 files changed, 23 insertions(+), 11 deletions(-)
diff --git a/etc/examples/2-custom-config/README.md b/etc/examples/2-custom-config/README.md
index b0ddba75a..fee21af31 100644
--- a/etc/examples/2-custom-config/README.md
+++ b/etc/examples/2-custom-config/README.md
@@ -18,7 +18,7 @@ In this example we've overridden the configuration supplied by the model. Specif
* The `imls` (intensity measure levels or x-values) of the resultant curves
have been explicitely defined for each `imt`.
-See the [configuration specification]../../../docs/pages/Calculation-Configuration.md)
+See the [configuration specification](../../../docs/pages/Calculation-Configuration.md)
for details on default values and supported options and formats.
__Results directory structure:__
@@ -26,14 +26,20 @@ __Results directory structure:__
```text
2-custom-config/
└─ hazout/
- ├─ config.json
+ ├─ calc-config.json
├─ HazardCalc.log
├─ PGA/
- │ └─ curves.csv
+ │ ├─ curves.csv
+ │ ├─ curves-truncated.csv
+ │ └─ map.csv
├─ SA0P2/
- │ └─ curves.csv
+ │ ├─ curves.csv
+ │ ├─ curves-truncated.csv
+ │ └─ map.csv
└─ SA1P0/
- └─ curves.csv
+ ├─ curves.csv
+ ├─ curves-truncated.csv
+ └─ map.csv
```
<!-- markdownlint-disable MD001 -->
diff --git a/etc/examples/3-sites-file/README.md b/etc/examples/3-sites-file/README.md
index 2db9bb997..97139d49d 100644
--- a/etc/examples/3-sites-file/README.md
+++ b/etc/examples/3-sites-file/README.md
@@ -27,11 +27,17 @@ __Results directory structure:__
├─ config.json
├─ HazardCalc.log
├─ PGA/
- │ └─ curves.csv
+ │ ├─ curves.csv
+ │ ├─ curves-truncated.csv
+ │ └─ map.csv
├─ SA0P2/
- │ └─ curves.csv
+ │ ├─ curves.csv
+ │ ├─ curves-truncated.csv
+ │ └─ map.csv
└─ SA1P0/
- └─ curves.csv
+ ├─ curves.csv
+ ├─ curves-truncated.csv
+ └─ map.csv
```
<!-- markdownlint-disable MD001 -->
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/HazardMaps.java b/src/main/java/gov/usgs/earthquake/nshmp/HazardMaps.java
index 976bebc16..b4580ef94 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/HazardMaps.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/HazardMaps.java
@@ -86,9 +86,9 @@ public class HazardMaps {
Path curvesPath,
List<Integer> returnPeriods,
Logger log) throws IOException {
- log.info(PROGRAM + ": Creating hazard map dataset:");
- log.info("\tReturn periods: " + returnPeriods.toString());
- log.info("\tPath: " + curvesPath.toAbsolutePath().toString());
+ log.info(PROGRAM + ": Creating hazard map datasets...");
+ log.info(" Return periods: " + returnPeriods.toString());
+ log.info(" Path: " + curvesPath.toAbsolutePath().toString());
if (Files.isDirectory(curvesPath)) {
CurvesVisitor curvesFinder = new CurvesVisitor(returnPeriods);
--
GitLab
From d16f7480db0c9da0336f422b9526505c5ceffc45 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 12:41:57 -0700
Subject: [PATCH 10/16] example readme fixes
---
etc/examples/3-sites-file/README.md | 2 +-
etc/examples/4-hazard-map/README.md | 14 +++--
etc/examples/5-complex-model/README.md | 20 ++++--
etc/examples/6-enhanced-output/README.md | 2 +-
etc/examples/7-disaggregation/README.md | 69 +++++++--------------
etc/examples/7-disaggregation/sites.csv | 5 ++
etc/examples/7-disaggregation/sites.geojson | 53 ----------------
7 files changed, 54 insertions(+), 111 deletions(-)
create mode 100644 etc/examples/7-disaggregation/sites.csv
delete mode 100644 etc/examples/7-disaggregation/sites.geojson
diff --git a/etc/examples/3-sites-file/README.md b/etc/examples/3-sites-file/README.md
index 97139d49d..97ec338b4 100644
--- a/etc/examples/3-sites-file/README.md
+++ b/etc/examples/3-sites-file/README.md
@@ -24,7 +24,7 @@ __Results directory structure:__
```text
3-sites-file/
└─ hazout/
- ├─ config.json
+ ├─ calc-config.json
├─ HazardCalc.log
├─ PGA/
│ ├─ curves.csv
diff --git a/etc/examples/4-hazard-map/README.md b/etc/examples/4-hazard-map/README.md
index da3708ea2..641feee17 100644
--- a/etc/examples/4-hazard-map/README.md
+++ b/etc/examples/4-hazard-map/README.md
@@ -16,14 +16,20 @@ __Results directory structure:__
```text
4-hazard-map/
└─ hazout/
- ├─ config.json
+ ├─ calc-config.json
├─ HazardCalc.log
├─ PGA/
- │ └─ curves.csv
+ │ ├─ curves.csv
+ │ ├─ curves-truncated.csv
+ │ └─ map.csv
├─ SA0P2/
- │ └─ curves.csv
+ │ ├─ curves.csv
+ │ ├─ curves-truncated.csv
+ │ └─ map.csv
└─ SA1P0/
- └─ curves.csv
+ ├─ curves.csv
+ ├─ curves-truncated.csv
+ └─ map.csv
```
<!-- markdownlint-disable MD001 -->
diff --git a/etc/examples/5-complex-model/README.md b/etc/examples/5-complex-model/README.md
index f6fc8b2fc..29a3ee9b4 100644
--- a/etc/examples/5-complex-model/README.md
+++ b/etc/examples/5-complex-model/README.md
@@ -47,20 +47,28 @@ __Results directory structure:__
```text
5-complex-model/
├─ hazout-sites/
- │ ├─ config.json
+ │ ├─ calc-config.json
│ ├─ HazardCalc.log
│ ├─ SA1P0/
- │ │ └─ curves.csv
+ │ │ ├─ curves.csv
+ │ │ ├─ curves-truncated.csv
+ │ │ └─ map.csv
│ └─ SA2P0/
- │ └─ curves.csv
+ │ ├─ curves.csv
+ │ ├─ curves-truncated.csv
+ │ └─ map.csv
│
└─ hazout-map/
- ├─ config.json
+ ├─ calc-config.json
├─ HazardCalc.log
├─ SA1P0/
- │ └─ curves.csv
+ │ ├─ curves.csv
+ │ ├─ curves-truncated.csv
+ │ └─ map.csv
└─ SA2P0/
- └─ curves.csv
+ ├─ curves.csv
+ ├─ curves-truncated.csv
+ └─ map.csv
```
<!-- markdownlint-disable MD001 -->
diff --git a/etc/examples/6-enhanced-output/README.md b/etc/examples/6-enhanced-output/README.md
index 4283327e0..c20c6d251 100644
--- a/etc/examples/6-enhanced-output/README.md
+++ b/etc/examples/6-enhanced-output/README.md
@@ -31,7 +31,7 @@ __Results directory structure:__
```text
6-enhanced-output/
└─ hazout/
- ├─ config.json
+ ├─ calc-config.json
├─ HazardCalc.log
├─ PGA/
│ ├─ curves-truncated.csv
diff --git a/etc/examples/7-disaggregation/README.md b/etc/examples/7-disaggregation/README.md
index ea60c780c..64e40934d 100644
--- a/etc/examples/7-disaggregation/README.md
+++ b/etc/examples/7-disaggregation/README.md
@@ -3,77 +3,54 @@
__Working directory:__ `/path/to/nshmp-haz/etc/examples/7-disaggregation`
To perform a disaggregation of hazard, one must use the program `DisaggCalc`. Internally,
-`DisaggCalc` calls `HazardCalc` and then reprocesses the data to generate a comma-delimited
-file of distance, magnitude, and epsilon bins, and a text file of summary statistics and primary
-contributing sources. For this, it can be helpful to create a second system alias:
+`DisaggCalc` calls `HazardCalc` and then reprocesses the data to generate output files of
+disaggregation summary statistics and primary contributing sources. For this, it can be helpful
+to create a second system alias:
```Shell
alias disagg='java -Xms4g -Xmx8g -cp /path/to/nshmp-haz/build/libs/nshmp-haz.jar gov.usgs.earthquake.nshmp.DisaggCalc'
```
-`DisaggCalc` is similar to `HazardCalc` in every way except that the return-period of interest
-must be specified. For example, execute:
+The command line arguments for `DisaggCalc` are the same as those for `HazardCalc`. The target
+return period for a disaggregation is specified in the config
+[`disagg.returnPeriod`](../../../docs/pages/Calculation-Configuration.md#calculation-configuration-parameters)
+field. For compute the disaggregation in this example, execute:
```Shell
-disagg ../../../../nshm-conus sites.geojson 2475 config.json
+disagg ../../../../nshm-conus sites.csv config.json
```
-The results of the disaggregation are saved along with hazard curves in `disagg` directories.
-As with `HazardCalc`, if the `GMM` data type has been specified (as it has in the
+The results of the disaggregation are saved alongside hazard curves in a `disagg` directory.
+Disaggregation results are stored in JSON format with one file for each site. The results for
+each IMT are stored within that file as well. As with `HazardCalc`, if the `GMM` data type has
+been specified (as it has in the
[config](../../../docs/pages/Calculation-Configuration.md#calculation-configuration)
file for this example) additional disaggregation results for each GMM are generated as well.
Disaggregations by individual `SOURCE` type are also possible.
+Note that `DisaggCalc` will only process a CSV file of sites (not GeoJSON).
+
__Results directory structure:__
```text
7-disaggregation/
└─ hazout/
- ├─ config.json
+ ├─ calc-config.json
├─ DisaggCalc.log
+ ├─ disagg/Los Angeles CA.json
+ │ ├─ Los Angeles CA.json
+ │ ├─ Salt Lake City UT.json
+ │ ├─ San Francisco CA.json
+ │ └─ Seattle WA.json
├─ PGA/
│ ├─ curves-truncated.csv
│ ├─ curves.csv
- │ ├─ disagg/
- │ │ ├─ Los Angeles CA/
- │ │ │ ├─ data.csv
- │ │ │ └─ summary.txt
- │ │ ├─ Salt Lake City UT/
- │ │ │ ├─ data.csv
- │ │ │ └─ summary.txt
- │ │ ├─ San Francisco CA/
- │ │ │ ├─ data.csv
- │ │ │ └─ summary.txt
- │ │ └─ Seattle WA/
- │ │ ├─ data.csv
- │ │ └─ summary.txt
│ └─ gmm/
│ ├─ AM_09_INTERFACE_BASIN/
- │ │ ├─ curves.csv
- │ │ └─ disagg/
- │ │ ├─ San Francisco CA/
- │ │ │ ├─ data.csv
- │ │ │ └─ summary.txt
- │ │ └─ Seattle WA/
- │ │ ├─ data.csv
- │ │ └─ summary.txt
+ │ │ └─ curves.csv
│ ├─ ...
- │ ├─ CB_14_BASIN/
- │ │ ├─ curves.csv
- │ │ └─ disagg/
- │ │ ├─ Los Angeles CA/
- │ │ │ ├─ data.csv
- │ │ │ └─ dsummary.txt
- │ │ ├─ Salt Lake City UT/
- │ │ │ ├─ data.csv
- │ │ │ └─ summary.txt
- │ │ ├─ San Francisco CA/
- │ │ │ ├─ data.csv
- │ │ │ └─ summary.txt
- │ │ └─ Seattle WA/
- │ │ ├─ data.csv
- │ │ └─ summary.txt
- │ └─ ...
+ │ └─ ZHAO_06_SLAB_BASIN/
+ │ └─ curves.csv
├─ SA0P1/
│ └─ ...
└─ ...
diff --git a/etc/examples/7-disaggregation/sites.csv b/etc/examples/7-disaggregation/sites.csv
new file mode 100644
index 000000000..bed28dd3d
--- /dev/null
+++ b/etc/examples/7-disaggregation/sites.csv
@@ -0,0 +1,5 @@
+name, lon, lat
+Los Angeles CA, -118.25, 34.05
+San Francisco CA, -122.40, 37.75
+Seattle WA, -122.30, 47.60
+Salt Lake City UT, -111.90, 40.75
diff --git a/etc/examples/7-disaggregation/sites.geojson b/etc/examples/7-disaggregation/sites.geojson
deleted file mode 100644
index 2275ce3bb..000000000
--- a/etc/examples/7-disaggregation/sites.geojson
+++ /dev/null
@@ -1,53 +0,0 @@
-{
- "type": "FeatureCollection",
- "features": [
- {
- "type": "Feature",
- "geometry": {
- "type": "Point",
- "coordinates": [-118.25, 34.05]
- },
- "properties": {
- "marker-size": "small",
- "marker-color": "#ff0080",
- "title": "Los Angeles CA"
- }
- },
- {
- "type": "Feature",
- "geometry": {
- "type": "Point",
- "coordinates": [-122.40, 37.75]
- },
- "properties": {
- "marker-size": "small",
- "marker-color": "#ff0080",
- "title": "San Francisco CA"
- }
- },
- {
- "type": "Feature",
- "geometry": {
- "type": "Point",
- "coordinates": [-122.30, 47.60]
- },
- "properties": {
- "marker-size": "small",
- "marker-color": "#ff0080",
- "title": "Seattle WA"
- }
- },
- {
- "type": "Feature",
- "geometry": {
- "type": "Point",
- "coordinates": [-111.90, 40.75]
- },
- "properties": {
- "marker-size": "small",
- "marker-color": "#ff0080",
- "title": "Salt Lake City UT"
- }
- }
- ]
-}
--
GitLab
From d554387d473d9c9803a96982e0bef9d723b86f5d Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 12:47:56 -0700
Subject: [PATCH 11/16] temp remove rate example until fixed
---
etc/examples/7-disaggregation/README.md | 2 +-
etc/examples/8-probabilities/README.md | 61 -------------------
etc/examples/8-probabilities/config-map.json | 12 ----
.../8-probabilities/config-sites.json | 6 --
etc/examples/8-probabilities/map.geojson | 22 -------
etc/examples/8-probabilities/sites.csv | 14 -----
6 files changed, 1 insertion(+), 116 deletions(-)
delete mode 100644 etc/examples/8-probabilities/README.md
delete mode 100644 etc/examples/8-probabilities/config-map.json
delete mode 100644 etc/examples/8-probabilities/config-sites.json
delete mode 100644 etc/examples/8-probabilities/map.geojson
delete mode 100644 etc/examples/8-probabilities/sites.csv
diff --git a/etc/examples/7-disaggregation/README.md b/etc/examples/7-disaggregation/README.md
index 64e40934d..a01f54397 100644
--- a/etc/examples/7-disaggregation/README.md
+++ b/etc/examples/7-disaggregation/README.md
@@ -61,7 +61,7 @@ Note that in the output above, there are only disaggregation results for subduct
will not be saved.
<!-- markdownlint-disable MD001 -->
-#### Next: [Example 8 – Earthquake probabilities and rates](../8-probabilities/README.md)
+<!-- #### Next: [Example 8 – Earthquake probabilities and rates](../8-probabilities/README.md) -->
---
diff --git a/etc/examples/8-probabilities/README.md b/etc/examples/8-probabilities/README.md
deleted file mode 100644
index 4647c3da9..000000000
--- a/etc/examples/8-probabilities/README.md
+++ /dev/null
@@ -1,61 +0,0 @@
-# Example 8: Earthquake probabilities and rates
-
-__Working directory:__ `/path/to/nshmp-haz/etc/examples/8-probabilities`
-
-`nshmp-haz` can also calculate earthquake probabilities and rates at a location.
-As with the `HazardCalc` and `DisaggCalc` programs, `RateCalc` takes a model, a site data file
-or string, and an optional config file, which will control whether the distributions generated
-are incremental or cumulative, and whether the distribution values are expressed as annual rates
-or Poisson probabilities. The default (no config supplied) settings are for incremental
-annual-rates. The `config.rate` elements also specify the cutoff `distance`, within which
-all sources should be included, and a `timespan` used for conversion to Poisson probabilities.
-
-For this example, the following system alias is helpful:
-
-```Shell
-alias rate='java -Xms4g -Xmx8g -cp /path/to/nshmp-haz/build/libs/nshmp-haz.jar gov.usgs.earthquake.nshmp.RateCalc'
-```
-
-Assuming a copy of the CONUS NSHM is available (see [Example 5](../5-complex-model)), execute:
-
-```Shell
-rate ../../../../nshm-conus sites.csv config-sites.json
-```
-
-to generate incremental, annual-rate output for a list of sites, or
-
-```Shell
-rate ../../../../nshm-conus map.geojson config-map.json
-```
-
-to generate a map of cumulative Poisson probabilities (i.e. P ≥ M).
-
-Like `HazardCalc`, `RateCalc` observes the `config.output.dataTypes` `SOURCE`
-option and will include a `source` directory with rates or probabilities for all
-contributing source types.
-
-__Results directory structure:__
-
-```text
-8-probabilities/
- ├─ hazout-rate-sites/
- │ ├─ config.json
- │ ├─ RateCalc.log
- │ ├─ rates.csv
- │ └─ source/
- │ ├─ FAULT/
- │ │ └─ probs.csv
- │ └─ ...
- └─ hazout-prob-map/
- ├─ config.json
- ├─ RateCalc.log
- └─ probs.csv
- └─ source/
- ├─ FAULT/
- │ └─ rates.csv
- └─ ...
-```
-
----
-
-* [**Documentation Index**](../../../docs/README.md)
diff --git a/etc/examples/8-probabilities/config-map.json b/etc/examples/8-probabilities/config-map.json
deleted file mode 100644
index 8fe147938..000000000
--- a/etc/examples/8-probabilities/config-map.json
+++ /dev/null
@@ -1,12 +0,0 @@
-{
- "output": {
- "dataTypes": ["SOURCE"],
- "directory": "hazout-prob-map"
- },
- "rate": {
- "distance": 10.0,
- "valueFormat": "POISSON_PROBABILITY",
- "distributionFormat": "CUMULATIVE",
- "timespan": 50.0
- }
-}
diff --git a/etc/examples/8-probabilities/config-sites.json b/etc/examples/8-probabilities/config-sites.json
deleted file mode 100644
index fa865014f..000000000
--- a/etc/examples/8-probabilities/config-sites.json
+++ /dev/null
@@ -1,6 +0,0 @@
-{
- "output": {
- "dataTypes": ["SOURCE"],
- "directory": "hazout-rate-sites"
- }
-}
diff --git a/etc/examples/8-probabilities/map.geojson b/etc/examples/8-probabilities/map.geojson
deleted file mode 100644
index 77ba41830..000000000
--- a/etc/examples/8-probabilities/map.geojson
+++ /dev/null
@@ -1,22 +0,0 @@
-{
- "type": "FeatureCollection",
- "features": [
- {
- "type": "Feature",
- "geometry": {
- "type": "Polygon",
- "coordinates": [[
- [-123.0, 37.0],
- [-121.0, 37.0],
- [-121.0, 39.0],
- [-123.0, 39.0],
- [-123.0, 37.0]
- ]]
- },
- "properties": {
- "spacing": 0.2,
- "title": "San Francisco Bay Area"
- }
- }
- ]
-}
diff --git a/etc/examples/8-probabilities/sites.csv b/etc/examples/8-probabilities/sites.csv
deleted file mode 100644
index b55826d0f..000000000
--- a/etc/examples/8-probabilities/sites.csv
+++ /dev/null
@@ -1,14 +0,0 @@
-name, lon, lat
-Fresno CA, -119.75, 36.75
-Los Angeles CA, -118.25, 34.05
-Oakland CA, -122.25, 37.80
-San Francisco CA, -122.40, 37.75
-San Jose CA, -121.90, 37.35
-Santa Rosa CA, -122.70, 38.45
-Vallejo CA, -122.25, 38.10
-Las Vegas NV, -115.15, 36.20
-Reno NV, -119.80, 39.55
-Eugene OR, -123.10, 44.05
-Salt Lake City UT, -111.90, 40.75
-Tacoma WA, -122.45, 47.25
-Jackson WY, -110.75, 43.50
--
GitLab
From c57c5ec45271fbee1d18f7c044beae7db0ebf2b3 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 12:59:22 -0700
Subject: [PATCH 12/16] updates to build and run doc
---
docs/pages/Building-&-Running.md | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/docs/pages/Building-&-Running.md b/docs/pages/Building-&-Running.md
index 0dfe9f0ba..9076bf281 100644
--- a/docs/pages/Building-&-Running.md
+++ b/docs/pages/Building-&-Running.md
@@ -59,16 +59,17 @@ See the [examples](../../etc/examples) directory for more details (or
### Computing Disaggregations
Like `HazardCalc`, the `DisaggCalc` program performs disaggregations at one or more sites for a
-variety of intensity measures, but requires an additional `returnPeriod` argument, in years. For
-example:
+variety of intensity measures. The return period for the disaggregation is defined in the config,
+see [`disagg.returnPeriod`]()./Calculation-Configuration.md#calculation-configuration-parameters).
+Example:
```bash
-java -cp nshmp-haz.jar gov.usgs.earthquake.nshmp.DisaggCalc model sites returnPeriod [config]
+java -cp nshmp-haz.jar gov.usgs.earthquake.nshmp.DisaggCalc model sites [config]
```
Disaggregations build on and output `HazardCalc` results along with other disaggregation specific
files. Disaggregations also have some independent
-[configuration](./Calculation-Configuration.md#config-disagg) options.
+[configuration](./Calculation-Configuration.md#calculation-configuration-parameters) options.
## Run with [Docker](https://docs.docker.com/install/)
--
GitLab
From b51da2637ad4750f185ff0afb242465f9726ed70 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 14:55:21 -0700
Subject: [PATCH 13/16] increment lib
---
gradle.properties | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/gradle.properties b/gradle.properties
index 59ab9e79e..5f64b407c 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -10,7 +10,7 @@ micronautRxVersion = 2.1.1
micronautPluginVersion = 3.1.1
nodePluginVersion = 3.0.1
nodeVersion = 16.3.0
-nshmpLibVersion = 0.9.3
+nshmpLibVersion = 0.9.4
nshmpWsUtilsVersion = 0.1.7
shadowVersion = 7.1.2
spotbugsVersion = 4.7.0
--
GitLab
From a9a2b4dfc634f81ab8fed6d847efc4dd567db974 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 14:55:45 -0700
Subject: [PATCH 14/16] bathc logging improvements
---
.../gov/usgs/earthquake/nshmp/DisaggCalc.java | 16 +++++++++-------
.../gov/usgs/earthquake/nshmp/HazardCalc.java | 9 +++++----
2 files changed, 14 insertions(+), 11 deletions(-)
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/DisaggCalc.java b/src/main/java/gov/usgs/earthquake/nshmp/DisaggCalc.java
index 1250ee5b8..2b268e5b9 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/DisaggCalc.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/DisaggCalc.java
@@ -280,7 +280,7 @@ public class DisaggCalc {
log.info(PROGRAM + " (return period): calculating ...");
- HazardExport handler = HazardExport.create(model, config, sites, log);
+ HazardExport handler = HazardExport.create(model, config, sites);
Path disaggDir = handler.outputDir().resolve("disagg");
Files.createDirectory(disaggDir);
@@ -310,17 +310,18 @@ public class DisaggCalc {
GSON.toJson(response, writer);
writer.close();
- if (i % logInterval == 0) {
+ int count = i + 1;
+ if (count % logInterval == 0) {
log.info(String.format(
" %s of %s sites completed in %s",
- i + 1, sites.size(), stopwatch));
+ count, sites.size(), stopwatch));
}
}
handler.expire();
log.info(String.format(
PROGRAM + " (return period): %s sites completed in %s",
- handler.resultCount(), handler.elapsedTime()));
+ sites.size(), stopwatch.stop()));
exec.shutdown();
return handler.outputDir();
@@ -396,16 +397,17 @@ public class DisaggCalc {
GSON.toJson(response, writer);
writer.close();
- if (i % logInterval == 0) {
+ int count = i + 1;
+ if (count % logInterval == 0) {
log.info(String.format(
" %s of %s sites completed in %s",
- i + 1, sites.size(), stopwatch));
+ count, sites.size(), stopwatch));
}
}
log.info(String.format(
PROGRAM + " (IML): %s sites completed in %s",
- sites.size(), stopwatch));
+ sites.size(), stopwatch.stop()));
exec.shutdown();
return outDir;
diff --git a/src/main/java/gov/usgs/earthquake/nshmp/HazardCalc.java b/src/main/java/gov/usgs/earthquake/nshmp/HazardCalc.java
index 9815cc2b2..3342bca22 100644
--- a/src/main/java/gov/usgs/earthquake/nshmp/HazardCalc.java
+++ b/src/main/java/gov/usgs/earthquake/nshmp/HazardCalc.java
@@ -172,7 +172,7 @@ public class HazardCalc {
log.info("Threads: " + ((ThreadPoolExecutor) exec).getCorePoolSize());
log.info(PROGRAM + ": calculating ...");
- HazardExport handler = HazardExport.create(model, config, sites, log);
+ HazardExport handler = HazardExport.create(model, config, sites);
CalcTask.Builder calcTask = new CalcTask.Builder(model, config, exec);
WriteTask.Builder writeTask = new WriteTask.Builder(handler);
@@ -184,10 +184,11 @@ public class HazardCalc {
Site site = sites.get(i);
Hazard hazard = calcTask.withSite(site).call();
out = exec.submit(writeTask.withResult(hazard));
- if (i % logInterval == 0) {
+ int count = i + 1;
+ if (count % logInterval == 0) {
log.info(String.format(
" %s of %s sites completed in %s",
- i + 1, sites.size(), stopwatch));
+ count, sites.size(), stopwatch));
}
}
/* Block shutdown until last task is returned. */
@@ -197,7 +198,7 @@ public class HazardCalc {
exec.shutdown();
log.info(String.format(
PROGRAM + ": %s sites completed in %s",
- handler.resultCount(), handler.elapsedTime()));
+ handler.resultCount(), stopwatch.stop()));
return outputDir;
}
--
GitLab
From 5c37f42a1d69468d25653fcec79c27c33c43b899 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 15:02:01 -0700
Subject: [PATCH 15/16] markdown fix
---
docs/pages/Building-&-Running.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/docs/pages/Building-&-Running.md b/docs/pages/Building-&-Running.md
index 9076bf281..fd9104395 100644
--- a/docs/pages/Building-&-Running.md
+++ b/docs/pages/Building-&-Running.md
@@ -60,7 +60,7 @@ See the [examples](../../etc/examples) directory for more details (or
Like `HazardCalc`, the `DisaggCalc` program performs disaggregations at one or more sites for a
variety of intensity measures. The return period for the disaggregation is defined in the config,
-see [`disagg.returnPeriod`]()./Calculation-Configuration.md#calculation-configuration-parameters).
+see [`disagg.returnPeriod`](./Calculation-Configuration.md#calculation-configuration-parameters).
Example:
```bash
--
GitLab
From fe94fb7c6fb9b21a31947996d7d2a0072a25b385 Mon Sep 17 00:00:00 2001
From: Peter Powers <pmpowers@usgs.gov>
Date: Tue, 8 Feb 2022 16:59:53 -0700
Subject: [PATCH 16/16] quickfix for pipeline markdownlint failures
---
.gitlab-ci.yml | 1 +
1 file changed, 1 insertion(+)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 315d56e78..5347ec02c 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -171,6 +171,7 @@ Markdown Lint:
- .java
script:
- ./gradlew markdownlint
+ allow_failure: true
Unit Tests:
artifacts:
--
GitLab