fits: honour UBYTE_FLAG_INFO column annotation

The FITS I/O table handlers now mark TFORMn=rB columns with UBYTE_FLAG_INFO on read, and if it's present on write the column is written with TFORMn=rB rather than rI.
Starlink · Feb 26, 2015 · d041658 · d041658
1 parent cc7abd5
commit d041658
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Showing 7 changed files with 165 additions and 61 deletions.
diff --git a/fits/src/main/uk/ac/starlink/fits/AbstractFitsTableWriter.java b/fits/src/main/uk/ac/starlink/fits/AbstractFitsTableWriter.java
@@ -26,6 +26,19 @@
 /**
  * Abstract table writer superclass designed for writing FITS tables.
  *
+ * <p>A couple of Auxiliary metadata items of the ColumnInfo metadata
+ * from written tables are respected:
+ * <ul>
+ * <li>{@link uk.ac.starlink.table.Tables#NULL_VALUE_INFO}:
+ *     sets the value of <code>TNULLn</code> "magic" blank value for
+ *     integer columns</li>
+ * <li>{@link uk.ac.starlink.table.Tables#UBYTE_FLAG_INFO}:
+ *     if set to <code>Boolean.TRUE</code> and if the column has content class
+ *     <code>Short</code> or <code>short[]</code>, the data will be written
+ *     as unsigned bytes (<code>TFORMn='B'</code>)
+ *     not 16-bit signed integers (<code>TFORMn='I'</code>).</li>
+ * </ul>
+ *
  * @author   Mark Taylor
  * @since    27 Jun 2006
  */

diff --git a/fits/src/main/uk/ac/starlink/fits/ArrayWriter.java b/fits/src/main/uk/ac/starlink/fits/ArrayWriter.java
@@ -3,6 +3,9 @@
 import java.io.DataOutput;
 import java.io.IOException;
 import java.lang.reflect.Array;
+import java.util.logging.Logger;
+import uk.ac.starlink.table.ColumnInfo;
+import uk.ac.starlink.table.Tables;
 
 /**
  * Object which knows how to write array data for a particular type 
@@ -16,6 +19,9 @@ abstract class ArrayWriter {
     private final char formatChar_;
     private final int nByte_;
 
+    private static final Logger logger_ =
+        Logger.getLogger( "uk.ac.starlink.fits" );
+
     /**
      * Constructor.
      *
@@ -74,14 +80,36 @@ public abstract void writeElement( DataOutput out, Object array,
     /**
      * Constructs a new ArrayWriter for a given array class.
      *
-     * @param   clazz   array class which this writer should be able to write
+     * @param   cinfo   column metadata describing the data
+     *                  which this writer should be able to write
      * @param   allowSignedByte  if true, bytes written as FITS signed bytes
      *          (TZERO=-128), if false bytes written as signed shorts
-     * @return  new ArrayWriter, or null if <code>clazz</code> can't be handled
+     * @return  new ArrayWriter, or null if <code>cinfo</code> can't be handled
      */
-    public static ArrayWriter createArrayWriter( Class clazz,
+    public static ArrayWriter createArrayWriter( ColumnInfo cinfo,
                                                  boolean allowSignedByte ) {
-
+        Class clazz = cinfo.getContentClass();
+        final boolean isUbyte =
+            Boolean.TRUE
+           .equals( cinfo.getAuxDatumValue( Tables.UBYTE_FLAG_INFO,
+                                            Boolean.class ) );
+
+        if ( isUbyte ) {
+            if ( clazz == short[].class ) {
+                return new NormalArrayWriter( 'B', 1,
+                                              new short[] { (short) 0 } ) {
+                    public void writeElement( DataOutput out, Object array,
+                                              int ix )
+                            throws IOException {
+                        out.writeByte( ((short[]) array)[ ix ] );
+                    }
+                };
+            }
+            else {
+                logger_.warning( "Ignoring " + Tables.UBYTE_FLAG_INFO
+                               + " on non-short[] column " + cinfo );
+            }
+        }
         if ( clazz == boolean[].class ) {
             return new ArrayWriter( 'L', 1 ) {
                 public void writeElement( DataOutput out, Object array, int ix )

diff --git a/fits/src/main/uk/ac/starlink/fits/BintableStarTable.java b/fits/src/main/uk/ac/starlink/fits/BintableStarTable.java
@@ -285,6 +285,10 @@ else if ( zIsInt && zInLongRange ) {
             cinfo.setContentClass( reader.getContentClass() );
             cinfo.setShape( reader.getShape() );
             cinfo.setElementSize( reader.getElementSize() );
+            if ( reader.isUnsignedByte() ) {
+                cinfo.setAuxDatum( new DescribedValue( Tables.UBYTE_FLAG_INFO,
+                                                       Boolean.TRUE ) );
+            }
             colReaders_[ icol ] = reader;
         }