#230 fix (wkt parsing and possible dead loop in grid cutting

AtlasOfLivingAustralia · Jan 29, 2024 · 2752d32 · 2752d32
1 parent f71f2e9
commit 2752d32
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Showing 5 changed files with 21 additions and 12 deletions.
diff --git a/build.gradle b/build.gradle
@@ -28,7 +28,7 @@ ext {
     drivers = ["firefox", "chrome", "chromeHeadless"]
 }
 
-version "2.1.1-SNAPSHOT"
+version "2.1.2-SNAPSHOT"
 group "au.org.ala"
 
 apply plugin: "eclipse"
@@ -107,6 +107,7 @@ dependencies {
     implementation "org.hibernate:hibernate-spatial"
     implementation "org.grails.plugins:gsp"
     implementation "io.micronaut:micronaut-inject-groovy"
+
     console "org.grails:grails-console"
     profile "org.grails.profiles:web"
     runtimeOnly "com.h2database:h2"

diff --git a/src/main/groovy/au/org/ala/spatial/intersect/SimpleRegion.groovy b/src/main/groovy/au/org/ala/spatial/intersect/SimpleRegion.groovy
@@ -198,6 +198,7 @@ class SimpleRegion implements Serializable {
         for (int i = 0; i < points.size(); i++) {
             pointsArray[i] = points.get(i)
         }
+        log.debug("Calculating BBox of a polygon")
         simpleregion.setPolygon(pointsArray)
         return simpleregion
     }
@@ -327,7 +328,6 @@ class SimpleRegion implements Serializable {
                     points[i] = points_[i]
                 }
             }
-
             /* bounding box setup */
             bounding_box = new double[2][2]
             bounding_box[0][0] = points[0]
@@ -963,7 +963,7 @@ class SimpleRegion implements Serializable {
         if (three_state_map == null) {
             three_state_map = new byte[height][width]
         }
-
+        log.debug("Calculating overlapped grids over polygons")
         double divx = (longitude2 - longitude1) / width
         double divy = (latitude2 - latitude1) / height
 
@@ -1018,7 +1018,8 @@ class SimpleRegion implements Serializable {
                 }
             } else { //sloped line
                 endlat = dy2
-                for (double k = (y + 1) * divy + latitude1; k < endlat; k += (int)(divy)) {
+                int kStep = Math.max(divy, 1)
+                for (double k = (y + 1) * divy + latitude1; k < endlat; k += kStep) {
                     //move in yDirection to get x
                     xcross = (k - intercept) / slope
                     icross = (int) ((xcross - longitude1) / divx)
@@ -1140,7 +1141,8 @@ class SimpleRegion implements Serializable {
                 }
             } else { //sloped line
                 endlat = dy2
-                for (double k = (y + 1) * divy + latitude1; k < endlat; k +=  (int)(divy)) {
+                int kStep = Math.max(divy, 1)
+                for (double k = (y + 1) * divy + latitude1; k < endlat; k +=  kStep) {
                     //move in yDirection to get x
                     xcross = (k - intercept) / slope
                     icross = (int) ((xcross - longitude1) / divx)

diff --git a/src/main/groovy/au/org/ala/spatial/intersect/SimpleShapeFile.groovy b/src/main/groovy/au/org/ala/spatial/intersect/SimpleShapeFile.groovy
@@ -29,6 +29,9 @@ import java.util.concurrent.CountDownLatch
 import java.util.concurrent.LinkedBlockingQueue
 import java.util.stream.Collectors
 
+import com.vividsolutions.jts.geom.*;
+import com.vividsolutions.jts.io.ParseException;
+import com.vividsolutions.jts.io.WKTReader;
 /**
  * SimpleShapeFile is a representation of a Shape File for
  * intersections with points
@@ -215,7 +218,7 @@ class SimpleShapeFile implements Serializable {
         } else if (pointsString.startsWith("MULTIPOLYGON")) {
             regions.addAll(parseMultipolygon(pointsString.substring(bracket3rd + 1, pointsString.length() - 3)))
         } else if (pointsString.startsWith("POLYGON")) {
-            regions.add(parsePolygon(pointsString.substring(bracket2nd + 1, pointsString.length() - 2)))
+           regions.add(parsePolygon(pointsString.substring(bracket2nd + 1, pointsString.length() - 2)))
         }
 
         if (regions.size() == 0) {

diff --git a/src/main/groovy/au/org/ala/spatial/process/Classification.groovy b/src/main/groovy/au/org/ala/spatial/process/Classification.groovy
@@ -27,7 +27,7 @@ import org.apache.commons.io.FileUtils
 class Classification extends SlaveProcess {
 
     void start() {
-        taskLog("Classification is about to start")
+        taskLog("Starting Classification")
         //list of layers
         List<String> layers = getInput('layer').toString().split(',')
         def envnameslist = new String[layers.size()]
@@ -49,9 +49,10 @@ class Classification extends SlaveProcess {
         def makeShapefile = getInput('shp')
 
         new File(getTaskPath()).mkdirs()
-
+        taskLog("Cutting Grids")
         def cutDataPath = cutGrid(envnameslist, resolution as String, regionEnvelope.region, regionEnvelope.envelope, null)
 
+        taskLog("Running aloc process")
         String[] cmd = ["java", "-Xmx" + String.valueOf(spatialConfig.aloc.xmx),
                         "-jar", spatialConfig.data.dir + '/modelling/aloc/aloc.jar',
                         cutDataPath, String.valueOf(groups), String.valueOf(spatialConfig.aloc.threads), getTaskPath()]

diff --git a/src/main/groovy/au/org/ala/spatial/process/SlaveProcess.groovy b/src/main/groovy/au/org/ala/spatial/process/SlaveProcess.groovy
@@ -572,6 +572,7 @@ class SlaveProcess {
 
             h = (int) Math.ceil((extents[1][1] - extents[0][1]) / res)
             w = (int) Math.ceil((extents[1][0] - extents[0][0]) / res)
+            log.debug("Calculating mask")
             mask = getRegionMask(extents, w, h, region)
         } else if (envelopes != null) {
             h = (int) Math.ceil((extents[1][1] - extents[0][1]) / res)
@@ -646,7 +647,7 @@ class SlaveProcess {
         String standardLayersDir = spatialConfig.data.dir + '/standard_layer/'
 
         File file = new File(standardLayersDir + resolution + '/' + layer + '.grd')
-        log.debug("Get grid from: " + file.path)
+        log.debug("loading grid from: " + file.path)
         //move up a resolution when the file does not exist at the target resolution
         try {
             while (!file.exists()) {
@@ -677,12 +678,13 @@ class SlaveProcess {
         }
 
         String layerPath = standardLayersDir + File.separator + resolution + File.separator + layer
+        taskLog("Loading " + layerPath)
 
         if (new File(layerPath + ".grd").exists()) {
             return layerPath
         } else {
-            taskLog("Fatal error: Cannot calcuate grid due to missing the layer file: " + layerPath)
-            log.error("Fatal error: Cannot calcuate grid due to missing the layer file: " + layerPath)
+            taskLog("Fatal error: Cannot calculate grid due to missing the layer file: " + layerPath)
+            log.error("Fatal error: Cannot calculate grid due to missing the layer file: " + layerPath)
             return null
         }
     }
@@ -938,7 +940,7 @@ class SlaveProcess {
                 }
             }
         }
-
+        log.debug("Writing grids to " + dir + layer)
         grid.writeGrid(dir + layer, dfiltered,
                 extents[0][0],
                 extents[0][1],