Merge "Omaha #5208 Decode and store scale and offset for pointset data." into omaha_16.2.2

Former-commit-id: ec013899b059f9ce267d64455735668936249c18

edexOsgi/com.raytheon.uf.common.dataplugin.pointset/src/com/raytheon/uf/common/dataplugin/pointset/PointSetConstants.java

@@ -29,13 +29,13 @@ package com.raytheon.uf.common.dataplugin.pointset;
  * SOFTWARE HISTORY
  * 
  * Date          Ticket#  Engineer  Description
- * ------------- -------- --------- --------------------------
+ * ------------- -------- --------- --------------------
  * Aug 28, 2015  4709     bsteffen  Initial creation
+ * Jan 21, 2016  5208     bsteffen  Add scale and offset
  * 
  * </pre>
  * 
  * @author bsteffen
- * @version 1.0
  */
 public class PointSetConstants {
 
@@ -60,4 +60,8 @@ public class PointSetConstants {
 
     public static final String LEVEL_TWO = LEVEL + ".leveltwovalue";
 
+    public static final String ADD_OFFSET = "add_offset";
+
+    public static final String SCALE_FACTOR = "scale_factor";
+
 }

edexOsgi/com.raytheon.uf.common.dataplugin.pointset/src/com/raytheon/uf/common/dataplugin/pointset/PointSetData.java

@@ -0,0 +1,158 @@
+/**
+ * This software was developed and / or modified by Raytheon Company,
+ * pursuant to Contract DG133W-05-CQ-1067 with the US Government.
+ * 
+ * U.S. EXPORT CONTROLLED TECHNICAL DATA
+ * This software product contains export-restricted data whose
+ * export/transfer/disclosure is restricted by U.S. law. Dissemination
+ * to non-U.S. persons whether in the United States or abroad requires
+ * an export license or other authorization.
+ * 
+ * Contractor Name:        Raytheon Company
+ * Contractor Address:     6825 Pine Street, Suite 340
+ *                         Mail Stop B8
+ *                         Omaha, NE 68106
+ *                         402.291.0100
+ * 
+ * See the AWIPS II Master Rights File ("Master Rights File.pdf") for
+ * further licensing information.
+ **/
+package com.raytheon.uf.common.dataplugin.pointset;
+
+import java.nio.Buffer;
+import java.nio.ByteBuffer;
+import java.nio.FloatBuffer;
+import java.nio.IntBuffer;
+import java.nio.ShortBuffer;
+
+import javax.measure.converter.AddConverter;
+import javax.measure.converter.MultiplyConverter;
+import javax.measure.converter.RationalConverter;
+import javax.measure.converter.UnitConverter;
+
+/**
+ * 
+ * Store the raw data for pointset. The primary structure is a {@link Buffer}
+ * containing numeric data for each point. This also has support for products
+ * that use scale and offset values in addition to the raw numeric data(This is
+ * for packing the data into bytes or shorts).
+ * 
+ * <pre>
+ * 
+ * SOFTWARE HISTORY
+ * 
+ * Date          Ticket#  Engineer  Description
+ * ------------- -------- --------- --------------------------
+ * Jan 20, 2016  5208     bsteffen  Initial creation
+ * 
+ * </pre>
+ * 
+ * @author bsteffen
+ */
+public class PointSetData {
+
+    private Buffer data;
+
+    private Float scale;
+
+    private Float offset;
+
+    public PointSetData() {
+
+    }
+
+    public PointSetData(Buffer data) {
+        this.data = data;
+    }
+
+    public Buffer getData() {
+        return data;
+    }
+
+    public void setData(Buffer data) {
+        this.data = data;
+    }
+
+    public Float getScale() {
+        return scale;
+    }
+
+    public void setScale(Float scale) {
+        this.scale = scale;
+    }
+
+    public Float getOffset() {
+        return offset;
+    }
+
+    public void setOffset(Float offset) {
+        this.offset = offset;
+    }
+
+    /**
+     * Converts the data using the specified converter. If there is a scale or
+     * offset present and the converter is a simple add or multiply then it is
+     * incorporated into the scale/offset and the data is left untouched, which
+     * keeps packed data small. For all other cases the data is converted to
+     * floats and the converter is applied to the data.
+     * 
+     * @param converter
+     */
+    public void convert(UnitConverter converter) {
+        if (data == null || converter == null
+                || converter == UnitConverter.IDENTITY) {
+            return;
+        }
+        if (scale != null
+                && (converter instanceof MultiplyConverter || converter instanceof RationalConverter)) {
+            this.scale = (float) converter.convert(this.scale);
+            if (this.offset != null) {
+                this.offset = (float) converter.convert(this.offset);
+            }
+        } else if (offset != null && converter instanceof AddConverter) {
+            this.offset = (float) converter.convert(this.offset);
+        } else {
+            FloatBuffer buffer = null;
+            if (this.data instanceof FloatBuffer) {
+                buffer = (FloatBuffer) this.data;
+            } else if (this.data instanceof ShortBuffer) {
+                ShortBuffer sbuffer = (ShortBuffer) this.data;
+                buffer = FloatBuffer.allocate(this.data.capacity());
+                for (int i = 0; i < buffer.capacity(); i += 1) {
+                    buffer.put(i, sbuffer.get(i));
+                }
+            } else if (this.data instanceof ByteBuffer) {
+                ByteBuffer bbuffer = (ByteBuffer) this.data;
+                buffer = FloatBuffer.allocate(this.data.capacity());
+                for (int i = 0; i < buffer.capacity(); i += 1) {
+                    buffer.put(i, bbuffer.get(i));
+                }
+            } else if (this.data instanceof IntBuffer) {
+                IntBuffer ibuffer = (IntBuffer) this.data;
+                buffer = FloatBuffer.allocate(this.data.capacity());
+                for (int i = 0; i < buffer.capacity(); i += 1) {
+                    buffer.put(i, ibuffer.get(i));
+                }
+            } else {
+                throw new IllegalStateException("Unsupported buffer of type: "
+                        + this.data.getClass().getSimpleName());
+            }
+            if (scale != null) {
+                for (int i = 0; i < buffer.capacity(); i += 1) {
+                    buffer.put(i, buffer.get(i) * scale);
+                }
+            }
+            if (offset != null) {
+                for (int i = 0; i < buffer.capacity(); i += 1) {
+                    buffer.put(i, buffer.get(i) + offset);
+                }
+            }
+            for (int i = 0; i < buffer.capacity(); i += 1) {
+                buffer.put(i, (float) converter.convert(buffer.get(i)));
+            }
+            this.scale = null;
+            this.offset = null;
+            this.data = buffer;
+        }
+    }
+}

edexOsgi/com.raytheon.uf.common.dataplugin.pointset/src/com/raytheon/uf/common/dataplugin/pointset/PointSetRecord.java

@@ -19,7 +19,6 @@
  **/
 package com.raytheon.uf.common.dataplugin.pointset;
 
-import java.nio.Buffer;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 
@@ -53,6 +52,7 @@ import com.raytheon.uf.common.serialization.annotations.DynamicSerializeElement;
  * Date          Ticket#  Engineer  Description
  * ------------- -------- --------- --------------------------
  * Aug 11, 2015  4709     bsteffen  Initial creation
+ * Jan 21, 2016  5208     bsteffen  Store data in new object.
  * 
  * </pre>
  * 
@@ -89,7 +89,8 @@ public class PointSetRecord extends PersistablePluginDataObject {
     @DynamicSerializeElement
     private String locationId;
 
-    private transient Buffer data;
+    private transient PointSetData data;
+
 
     public String getDatasetId() {
         return datasetId;
@@ -123,11 +124,11 @@ public class PointSetRecord extends PersistablePluginDataObject {
         this.locationId = locationId;
     }
 
-    public Buffer getData() {
+    public PointSetData getData() {
         return data;
     }
 
-    public void setData(Buffer data) {
+    public void setData(PointSetData data) {
         this.data = data;
     }
 

edexOsgi/com.raytheon.uf.edex.plugin.pointset.netcdf/src/com/raytheon/uf/edex/plugin/pointset/netcdf/PointSetNetcdfDecoder.java

@@ -48,6 +48,7 @@ import ucar.nc2.NetcdfFile;
 import ucar.nc2.Variable;
 
 import com.raytheon.uf.common.dataplugin.level.LevelFactory;
+import com.raytheon.uf.common.dataplugin.pointset.PointSetData;
 import com.raytheon.uf.common.dataplugin.pointset.PointSetLocation;
 import com.raytheon.uf.common.dataplugin.pointset.PointSetRecord;
 import com.raytheon.uf.common.dataplugin.pointset.triangulate.DelauneyTriangulator;
@@ -56,7 +57,7 @@ import com.raytheon.uf.common.datastorage.StorageException;
 import com.raytheon.uf.common.localization.IPathManager;
 import com.raytheon.uf.common.localization.LocalizationFile;
 import com.raytheon.uf.common.localization.exception.LocalizationException;
-import com.raytheon.uf.common.parameter.lookup.ParameterLookup;
+import com.raytheon.uf.edex.netcdf.decoder.util.NetcdfDecoderUtils;
 import com.raytheon.uf.edex.netcdf.description.VariableDescription;
 import com.raytheon.uf.edex.netcdf.description.exception.InvalidDescriptionException;
 import com.raytheon.uf.edex.plugin.pointset.netcdf.description.PointSetProductDescriptions;
@@ -79,8 +80,10 @@ import com.raytheon.uf.edex.plugin.pointset.netcdf.description.TriangulationDesc
  * SOFTWARE HISTORY
  * 
  * Date          Ticket#  Engineer  Description
- * ------------- -------- --------- --------------------------
+ * ------------- -------- --------- --------------------------------------------
  * Aug 11, 2015  4709     bsteffen  Initial creation
+ * Jan 21, 2016  5208     bsteffen  Decode scale, offset, units, long_name when
+ *                                  they are present
  * 
  * </pre>
  * 
@@ -103,15 +106,10 @@ public class PointSetNetcdfDecoder {
 
     private LevelFactory levelFactory;
 
-    private ParameterLookup parameterLookup;
-
     public PointSetRecord[] decode(File file) {
         if (levelFactory == null) {
             levelFactory = LevelFactory.getInstance();
         }
-        if (parameterLookup == null) {
-            parameterLookup = ParameterLookup.getInstance();
-        }
         try {
             NetcdfFile netcdfFile = NetcdfFile.open(file.getAbsolutePath());
             Map<String, String> locationCache = new HashMap<String, String>();
@@ -244,7 +242,7 @@ public class PointSetNetcdfDecoder {
             }
         }
 
-        PointSetRecord record = description.getRecord(file, parameterLookup,
+        PointSetRecord record = description.getRecord(file,
                 levelFactory);
         if (record == null) {
             if (debug) {
@@ -309,7 +307,27 @@ public class PointSetNetcdfDecoder {
                     dataVarName, dataType);
             return null;
         }
-        record.setData(numericData);
+
+        Attribute longNameAttribute = dataVariable.findAttribute("long_name");
+        if (longNameAttribute != null) {
+            record.getParameter().setName(longNameAttribute.getStringValue());
+        }
+        Attribute unitsAttribute = dataVariable.findAttribute("units");
+        if (unitsAttribute != null) {
+            record.getParameter()
+                    .setUnitString(unitsAttribute.getStringValue());
+        }
+        PointSetData data = new PointSetData(numericData);
+
+        Number scale = NetcdfDecoderUtils.getScaleFactor(dataVariable);
+        if (scale != NetcdfDecoderUtils.DEFAULT_SCALE_FACTOR) {
+            data.setScale(scale.floatValue());
+        }
+        Number offset = NetcdfDecoderUtils.getAddOffset(dataVariable);
+        if (offset != NetcdfDecoderUtils.DEFAULT_ADD_OFFSET) {
+            data.setOffset(offset.floatValue());
+        }
+        record.setData(data);
 
         StringBuilder locationKeyBuilder = new StringBuilder();
         lonVariable.getNameAndDimensions(locationKeyBuilder);
@@ -377,19 +395,19 @@ public class PointSetNetcdfDecoder {
         PointSetProductDescriptions descriptions = new PointSetProductDescriptions();
         for (LocalizationFile file : files) {
             logger.info("Loading pointset data description from "
-                    + file.getName());
+                    + file.getPath());
             try (InputStream inputStream = file.openInputStream()) {
                 PointSetProductDescriptions unmarshalled = JAXB.unmarshal(
                         inputStream, PointSetProductDescriptions.class);
                 for (ProductDescription description : unmarshalled
                         .getDescriptions()) {
-                    if (validate(file.getName(), description)) {
+                    if (validate(file.getPath(), description)) {
                         descriptions.addDescription(description);
                     }
                 }
             } catch (LocalizationException | IOException e) {
                 logger.error("Unable to load product descriptions from {}",
-                        file.getName(), e);
+                        file.getPath(), e);
             }
         }
         this.descriptions = descriptions;
@@ -403,10 +421,6 @@ public class PointSetNetcdfDecoder {
         this.levelFactory = levelFactory;
     }
 
-    public void setParameterLookup(ParameterLookup parameterLookup) {
-        this.parameterLookup = parameterLookup;
-    }
-
     protected boolean validate(String fileName, ProductDescription description) {
         VariableDescription data = description.getData();
         if (data == null) {

edexOsgi/com.raytheon.uf.edex.plugin.pointset.netcdf/src/com/raytheon/uf/edex/plugin/pointset/netcdf/description/ProductDescription.java

@@ -30,7 +30,7 @@ import ucar.nc2.NetcdfFile;
 import com.raytheon.uf.common.dataplugin.level.Level;
 import com.raytheon.uf.common.dataplugin.level.LevelFactory;
 import com.raytheon.uf.common.dataplugin.pointset.PointSetRecord;
-import com.raytheon.uf.common.parameter.lookup.ParameterLookup;
+import com.raytheon.uf.common.parameter.Parameter;
 import com.raytheon.uf.common.time.DataTime;
 import com.raytheon.uf.edex.netcdf.description.AbstractFieldDescription;
 import com.raytheon.uf.edex.netcdf.description.AttributeDescription;
@@ -52,8 +52,9 @@ import com.raytheon.uf.edex.plugin.pointset.netcdf.PointSetNetcdfDecoder;
  * SOFTWARE HISTORY
  * 
  * Date          Ticket#  Engineer  Description
- * ------------- -------- --------- --------------------------
+ * ------------- -------- --------- ----------------------------------
  * Aug 11, 2015  4709     bsteffen  Initial creation
+ * Jan 21, 2016  5208     bsteffen  Move parameter persistence to dao
  * 
  * </pre>
  * 
@@ -183,15 +184,14 @@ public class ProductDescription {
      * Extract the the datasetId, parameter, level and datatime from the file
      * using the attributes contained in this description.
      */
-    public PointSetRecord getRecord(NetcdfFile file,
+    public PointSetRecord getRecord(NetcdfFile file, LevelFactory levelFactory)
-            ParameterLookup parameterLookup, LevelFactory levelFactory)
             throws InvalidDescriptionException {
         String datasetId = this.datasetId.getString(file);
         if (datasetId == null) {
             return null;
         }
-        String parameter = this.parameter.getString(file);
+        String parameterAbbrev = this.parameter.getString(file);
-        if (parameter == null) {
+        if (parameterAbbrev == null) {
             return null;
         }
         Level level = this.level.getLevel(file, levelFactory);
@@ -204,7 +204,7 @@ public class ProductDescription {
         }
         PointSetRecord record = new PointSetRecord();
         record.setDatasetId(datasetId);
-        record.setParameter(parameterLookup.getParameter(parameter));
+        record.setParameter(new Parameter(parameterAbbrev));
         record.setLevel(level);
         record.setDataTime(dataTime);
         return record;

edexOsgi/com.raytheon.uf.edex.plugin.pointset/META-INF/MANIFEST.MF

@@ -8,4 +8,6 @@ Bundle-RequiredExecutionEnvironment: JavaSE-1.7
 Require-Bundle: com.raytheon.uf.common.dataplugin;bundle-version="1.14.0",
  com.raytheon.uf.common.dataplugin.pointset;bundle-version="1.15.0",
  com.raytheon.uf.common.datastorage;bundle-version="1.15.0",
- com.raytheon.uf.edex.database;bundle-version="1.15.0"
+ com.raytheon.uf.edex.database;bundle-version="1.15.0",
+ javax.measure;bundle-version="1.0.0",
+ com.raytheon.uf.common.status;bundle-version="1.15.0"

edexOsgi/com.raytheon.uf.edex.plugin.pointset/src/com/raytheon/uf/edex/plugin/pointset/PointSetDao.java

@@ -20,12 +20,25 @@
 package com.raytheon.uf.edex.plugin.pointset;
 
 import java.nio.Buffer;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
+import javax.measure.converter.UnitConverter;
+
+import com.raytheon.uf.common.dataplugin.PluginDataObject;
 import com.raytheon.uf.common.dataplugin.PluginException;
 import com.raytheon.uf.common.dataplugin.persist.IPersistable;
+import com.raytheon.uf.common.dataplugin.pointset.PointSetConstants;
+import com.raytheon.uf.common.dataplugin.pointset.PointSetData;
 import com.raytheon.uf.common.dataplugin.pointset.PointSetRecord;
 import com.raytheon.uf.common.datastorage.DataStoreFactory;
 import com.raytheon.uf.common.datastorage.IDataStore;
+import com.raytheon.uf.common.datastorage.StorageStatus;
+import com.raytheon.uf.common.datastorage.records.IDataRecord;
+import com.raytheon.uf.common.parameter.Parameter;
+import com.raytheon.uf.common.parameter.lookup.ParameterLookup;
 import com.raytheon.uf.edex.database.plugin.PluginDao;
 
 /**
@@ -37,8 +50,9 @@ import com.raytheon.uf.edex.database.plugin.PluginDao;
  * SOFTWARE HISTORY
  * 
  * Date          Ticket#  Engineer  Description
- * ------------- -------- --------- --------------------------
+ * ------------- -------- --------- -----------------------
  * Aug 11, 2015  4709     bsteffen  Initial creation
+ * Jan 21, 2016  5208     bsteffen  Store scale and offset
  * 
  * </pre>
  * 
@@ -54,14 +68,78 @@ public class PointSetDao extends PluginDao {
         super("pointset");
     }
 
+    @Override
+    public PluginDataObject[] persistToDatabase(PluginDataObject... records) {
+        return super.persistToDatabase(verifyRecords(records));
+    }
+
+    @Override
+    public StorageStatus persistToHDF5(PluginDataObject... records)
+            throws PluginException {
+        return super.persistToHDF5(verifyRecords(records));
+    }
+
+    private PluginDataObject[] verifyRecords(PluginDataObject... records) {
+        List<PluginDataObject> toPersist = new ArrayList<PluginDataObject>(
+                records.length);
+        for (PluginDataObject record : records) {
+            PointSetRecord rec = (PointSetRecord) record;
+            if (validateParameter(rec)) {
+                toPersist.add(rec);
+            }
+        }
+        return toPersist.toArray(new PointSetRecord[toPersist.size()]);
+    }
+
+    protected boolean validateParameter(PointSetRecord record) {
+        Parameter parameter = record.getParameter();
+        boolean result = true;
+        if (parameter == null) {
+            result = false;
+        } else if (parameter.getName() == null) {
+            result = false;
+        } else if (parameter.getName().equals("Missing")) {
+            result = false;
+        } else {
+            Parameter dbParameter = ParameterLookup.getInstance().getParameter(
+                    parameter, true);
+            if (!parameter.equals(dbParameter)) {
+                UnitConverter converter = Parameter.compareUnits(parameter,
+                        dbParameter);
+                    record.getData().convert(converter);
+            }
+            record.setParameter(dbParameter);
+        }
+        if (!result) {
+            logger.info("Discarding record due to missing or unknown parameter mapping: "
+                    + record);
+        }
+        return result;
+    }
+
     @Override
     protected IDataStore populateDataStore(IDataStore dataStore,
             IPersistable obj) throws Exception {
         if (obj instanceof PointSetRecord) {
             PointSetRecord points = (PointSetRecord) obj;
-            Buffer data = points.getData();
+            PointSetData data = points.getData();
-            dataStore.addDataRecord(DataStoreFactory.createStorageRecord(
+            Buffer buffer = data.getData();
-                    "Data", points.getDataURI(), data.array()));
+            IDataRecord dataRecord = DataStoreFactory.createStorageRecord(
+                    "Data", points.getDataURI(), buffer.array());
+            if (data.getOffset() != null || data.getScale() != null) {
+                Map<String, Object> dataAttributes = new HashMap<>();
+                if (data.getOffset() != null) {
+                    dataAttributes.put(PointSetConstants.ADD_OFFSET,
+                            data.getOffset());
+                }
+                if (data.getScale() != null) {
+                    dataAttributes.put(PointSetConstants.SCALE_FACTOR,
+                            data.getScale());
+                }
+
+                dataRecord.setDataAttributes(dataAttributes);
+            }
+            dataStore.addDataRecord(dataRecord);
         } else if (obj != null) {
             throw new IllegalArgumentException("Cannot handle "
                     + obj.getClass().getSimpleName());