cutout for vlkb: implements nullValuesCount when using 'vlkb' exec

data-access/servlet/src/main/java/datasets/Cutout.java

@@ -19,7 +19,7 @@ public interface Cutout
    public CutResult doFile(String relPathname, int hdunum, Pos pos, Band band, Time time, Pol pol,
          boolean countNullValues, FitsCard[] extraCards)
          throws IOException, InterruptedException;
-;
+
 
 }
 

data-access/servlet/src/main/java/datasets/CutoutImpl.java

@@ -47,14 +47,6 @@ class CutoutImpl implements Cutout
       this.settings = settings;
    }
 
-/*
-   public DatasetsImpl(Settings settings, Subsurvey[] subsurveys)
-   {
-      LOGGER.info("trace DatasetsImpl(settings, subsurveys)");
-      this.settings = settings;
-      this.subsurveys = subsurveys;
-   }
-*/
 
    private String genRegionForVlkbOverlapCmd(Pos pos, Band band)
    {
@@ -182,6 +174,55 @@ class CutoutImpl implements Cutout
       }
 
 
+
+   private NullValueCount doCountNullValues(String absPathname, int hdunum)
+      throws IOException, InterruptedException
+      {
+         ByteArrayOutputStream bos = new ByteArrayOutputStream();
+         if(bos == null)
+            throw new AssertionError("byte output stream for bounds was not created, is null");
+
+         String[] cmdBounds = new String[3];
+         cmdBounds[0] = "/usr/local/bin/vlkb";
+         cmdBounds[1] = "nullvals";
+         cmdBounds[2] = absPathname;
+
+         ExecCmd exec = new ExecCmd();
+         exec.doRun(bos, cmdBounds);
+         LOGGER.info("exec NullVals exitValue: " + exec.exitValue);
+
+         bos.close();
+
+         boolean hasResult = (exec.exitValue == 0);
+         if(hasResult)
+         {
+            String nullValsString = new String(bos.toByteArray());
+            LOGGER.info("vlkb nullvals: " + nullValsString);
+
+            if((nullValsString != null) && nullValsString.trim().isEmpty())
+            {
+               throw new AssertionError("'vlkb nullvals' returned empty string");
+            }
+
+            // parse result: '<fill-ratio> <nullvals-count> <tot-count>'
+
+            String[] splitStr = nullValsString.trim().split("\\s+");
+            if(splitStr.length != 3) throw new AssertionError("'vlkb nullvals' did not return 3 numbers but: " + nullValsString);
+
+            NullValueCount nvc = new NullValueCount();
+            nvc.percent = Double.parseDouble(splitStr[0]);
+            nvc.nullCount = Long.parseLong(splitStr[1]);
+            nvc.totalCount = Long.parseLong(splitStr[2]);
+            return nvc;
+         } 
+         else
+         {
+            throw new AssertionError("'vlkb nullvals' exited without results for: " + absPathname);
+         }
+      }
+
+
+
    public CutResult doFile(String relPathname, int hdunum,
          Pos pos, Band band, Time time, Pol pol,
          boolean countNullValues, FitsCard[] extraCards)
@@ -210,7 +251,12 @@ class CutoutImpl implements Cutout
 
          if(countNullValues)
          {
-               LOGGER.info("NullValuesCount not implemented when used with Cutout::doStream()");
+              cutResult.nullValueCount = doCountNullValues(absSubimgPathname, 1);
+         }
+
+         if(extraCards == null || (extraCards.length < 1))
+         {
+            LOGGER.info("Adding extraCards to cut-file not implemented when using 'vlkb' exec (implemented in engine vlkbd/AMQP)");
          }
       }
       else