Merge pull request #1362 from haileyajohnson/dsgSubsetWriters

Dsg subset writers

Author: tdrwenski

cdm/core/src/main/java/ucar/nc2/ft/point/writer/CFPointWriter.java

@@ -266,26 +266,31 @@ private static int writeStationProfileFeatureCollection(FeatureDatasetPoint data
       List<Variable> extraVariables = new ArrayList<>();
       List<StationFeature> flattenFeatures = new ArrayList<>();
 
+      int countProfiles = 0;
+      int name_strlen = 0;
       for (DsgFeatureCollection dsgFeatures : dataset.getPointFeatureCollectionList()) {
         extraVariables.addAll(dsgFeatures.getExtraVariables());
         flattenFeatures.addAll(((StationProfileFeatureCollection) dsgFeatures).getStationFeatures());
+        for (StationProfileFeature station : (StationProfileFeatureCollection) dsgFeatures) {
+          name_strlen = Math.max(name_strlen, station.getName().length());
+          for (ProfileFeature fp : station) {
+            countProfiles++;
+          }
+        }
       }
 
       cfWriter.setExtraVariables(extraVariables);
       cfWriter.setStations(flattenFeatures);
-      cfWriter.setFeatureAuxInfo(0, 0);
+      cfWriter.setFeatureAuxInfo(countProfiles, name_strlen);
       cfWriter.writeHeader(flattenFeatures);
 
       int count = 0;
       for (DsgFeatureCollection featureCollection : dataset.getPointFeatureCollectionList()) {
-        cfWriter.resetObsIndex();
-        for (StationFeature station : ((StationProfileFeatureCollection) featureCollection).getStationFeatures()) {
-          StationProfileFeature spf = (StationProfileFeature) station;
-          cfWriter.resetProfileIndex();
-          for (ProfileFeature pf : spf) {
+        for (StationProfileFeature station : (StationProfileFeatureCollection) featureCollection) {
+          for (ProfileFeature pf : station) {
             if (pf.getTime() == null)
               continue; // assume this means its an "incomplete multidimensional"
-            count += cfWriter.writeProfile(spf, pf);
+            count += cfWriter.writeProfile(station, pf);
             if (debug && count % 100 == 0)
               logger.debug(String.format("%d ", count));
             if (debug && count % 1000 == 0)

cdm/core/src/main/java/ucar/nc2/ft/point/writer/WriterCFStationCollection.java

@@ -109,7 +109,7 @@ public void writeHeader(List<StationFeature> stns, @Nullable StationPointFeature
 
     llbb = CFPointWriterUtils.getBoundingBox(stnList); // gets written in super.finish();
 
-    altitudeCoordinateName = altName;
+    altitudeCoordinateName = stationAltName;
     coords.add(VariableSimpleBuilder
         .makeScalar(stationIndexName, "station index for this observation record", null, DataType.INT)
         .addAttribute(CF.INSTANCE_DIMENSION, stationDimName).build());

cdm/core/src/main/java/ucar/nc2/ft/point/writer/WriterCFStationProfileCollection.java

@@ -6,7 +6,6 @@
 package ucar.nc2.ft.point.writer;
 
 import com.google.common.collect.ImmutableList;
-import com.google.common.collect.Iterables;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import ucar.ma2.*;
@@ -94,11 +93,16 @@ public int writeProfile(StationProfileFeature spf, ProfileFeature profile) throw
       writeObsData(pf);
       count++;
     }
+    Integer stnIndex = stationIndexMap.get(spf.getName());
+    if (stnIndex == null) {
+      log.warn("BAD station {}", spf.getName());
+    } else {
+      writeProfileData(stnIndex, profile, count);
+    }
     return count;
   }
 
   public void writeHeader(List<StationFeature> stations) throws IOException {
-
     List<VariableSimpleIF> obsCoords = new ArrayList<>();
     List<PointFeatureCollection> flattenStations = new ArrayList<>();
     List<StructureData> featureData = new ArrayList<>();
@@ -133,35 +137,10 @@ public void writeHeader(List<StationFeature> stations) throws IOException {
     for (StationFeature sf : stnList) {
       writeStationData(sf);
       stationIndexMap.put(sf.getName(), count);
-      for (ProfileFeature p : (StationProfileFeature) sf) {
-        int countPoints = 0;
-        if (p.size() >= 0) {
-          countPoints += p.size();
-        } else {
-          countPoints += Iterables.size(p);
-        }
-        writeProfileData(count, p, countPoints);
-      }
       count++;
     }
   }
 
-  @Override
-  public void setFeatureAuxInfo(int nfeatures, int id_strlen) {
-    int countProfiles = 0;
-    int name_strlen = 0;
-    for (StationFeature s : stnList) {
-      name_strlen = Math.max(name_strlen, s.getName().length());
-      if (((StationProfileFeature) s).size() >= 0)
-        countProfiles += ((StationProfileFeature) s).size();
-      else {
-        countProfiles += Iterables.size(((StationProfileFeature) s));
-      }
-    }
-    this.nfeatures = countProfiles;
-    this.id_strlen = name_strlen;
-  }
-
   protected void makeFeatureVariables(List<StructureData> stnDataStructs, boolean isExtended) {
     // add the dimensions : extended model can use an unlimited dimension
     // Dimension stationDim = isExtended ? writer.addDimension(null, stationDimName, 0, true, true, false) :
@@ -265,10 +244,6 @@ protected void makeMiddleVariables(List<StructureData> profileDataStructs, boole
 
   private int profileRecno;
 
-  protected void resetProfileIndex() {
-    profileRecno = 0;
-  }
-
   public void writeProfileData(int stnIndex, ProfileFeature profile, int nobs) throws IOException {
     trackBB(profile.getLatLon(), profile.getTime());
 
@@ -292,10 +267,6 @@ public void writeProfileData(int stnIndex, ProfileFeature profile, int nobs) thr
 
   private int obsRecno;
 
-  protected void resetObsIndex() {
-    obsRecno = 0;
-  }
-
   public void writeObsData(PointFeature pf) throws IOException {
     StructureMembers.Builder smb = StructureMembers.builder().setName("Coords");
     smb.addMemberScalar(pf.getFeatureCollection().getTimeName(), null, null, DataType.DOUBLE, pf.getObservationTime());

cdm/core/src/main/java/ucar/nc2/ft/point/writer2/WriterCFPointAbstract.java

@@ -218,7 +218,7 @@ protected void writeHeader(List<VariableSimpleIF> obsCoords,
 
         Formatter coordNames = new Formatter().format("%s %s %s", stnFeature.getTimeName(), latName, lonName);
         if (!Double.isNaN(pointFeat.getLocation().getAltitude())) {
-          coordNames.format(" %s", stnFeature.getAltName());
+          coordNames.format(" %s", altitudeCoordinateName);
         }
         if (isExtendedModel) {
           addDataVariablesExtended(recordb, obsData, coordNames.toString());

cdm/core/src/main/java/ucar/nc2/ft/point/writer2/WriterCFStationProfileCollection.java

@@ -139,10 +139,8 @@ protected void writeHeader(List<StationFeature> stations) throws IOException {
       stationIndexMap.put(sf.getName(), count);
       for (ProfileFeature p : (StationProfileFeature) sf) {
         int countPoints = 0;
-        if (p.size() >= 0) {
-          countPoints += p.size();
-        } else {
-          countPoints += Iterables.size(p);
+        for (PointFeature pf : p) {
+          countPoints++;
         }
         writeProfileData(count, p, countPoints);
       }