Memoizer: Persist caching to sub readers

components/formats-bsd/src/loci/formats/Memoizer.java

@@ -46,6 +46,8 @@
 import loci.common.services.DependencyException;
 import loci.common.services.ServiceException;
 import loci.common.services.ServiceFactory;
+import loci.formats.in.DynamicMetadataOptions;
+import loci.formats.in.MetadataOptions;
 import loci.formats.meta.MetadataRetrieve;
 import loci.formats.meta.MetadataStore;
 import loci.formats.services.OMEXMLService;
@@ -430,6 +432,7 @@ public void saveStop() throws IOException {
    */
   public Memoizer() {
     this(DEFAULT_MINIMUM_ELAPSED);
+    configure(reader.getMetadataOptions());
   }
 
   /**
@@ -444,6 +447,7 @@ public Memoizer() {
   public Memoizer(long minimumElapsed) {
     this(minimumElapsed, null);
     this.doInPlaceCaching = true;
+    configure(reader.getMetadataOptions());
   }
 
   /**
@@ -462,6 +466,7 @@ public Memoizer(long minimumElapsed, File directory) {
     super();
     this.minimumElapsed = minimumElapsed;
     this.directory = directory;
+    configure(reader.getMetadataOptions());
   }
 
   /**
@@ -474,6 +479,7 @@ public Memoizer(long minimumElapsed, File directory) {
    */
   public Memoizer(IFormatReader r) {
     this(r, DEFAULT_MINIMUM_ELAPSED);
+    configure(reader.getMetadataOptions());
   }
 
   /**
@@ -490,6 +496,7 @@ public Memoizer(IFormatReader r) {
   public Memoizer(IFormatReader r, long minimumElapsed) {
     this(r, minimumElapsed, null);
     this.doInPlaceCaching = true;
+    configure(reader.getMetadataOptions());
   }
 
   /**
@@ -509,8 +516,57 @@ public Memoizer(IFormatReader r, long minimumElapsed, File directory) {
     super(r);
     this.minimumElapsed = minimumElapsed;
     this.directory = directory;
+    configure(reader.getMetadataOptions());
   }
 
+  /**
+   * Used to inject all the properties necessary for {@link Memoizer}
+   * creation into {@link MetadataOptions}. This is called by every
+   * constructor so that {@link IFormatReader} instances created
+   * internally can also make use of memoization.
+   *
+   * @param options
+   */
+  public void configure(MetadataOptions options) {
+    String k = Memoizer.class.getName();
+    if (options instanceof DynamicMetadataOptions) {
+      ((DynamicMetadataOptions) options).setFile(k + ".cacheDirectory", this.directory);
+      ((DynamicMetadataOptions) options).setBoolean(k + ".inPlace", this.doInPlaceCaching);
+      ((DynamicMetadataOptions) options).setLong(k + ".minimumElapsed", this.minimumElapsed);
+    }
+  }
+
+  /**
+   * If {@link MetadataOptions} have been configured per
+   * {@link #configure(MetadataOptions)}, then wrap the given
+   * {@link IFormatReader} with a {@link Memoizer} instance and return.
+   * Otherwise, return the {@link IFormatReader} unchanged.
+   *
+   * @param options If null, return the reader
+   * @param r
+   * @return Either a {@link Memoizer} or the {@link IFormatReader} argument.
+   */
+  public static IFormatReader wrap(MetadataOptions options, IFormatReader r) {
+    if (options == null || !(options instanceof DynamicMetadataOptions)) {
+      return r;
+    }
+    String k = Memoizer.class.getName();
+    Long elapsed = ((DynamicMetadataOptions) options).getLong(k + ".minimumElapsed");
+    Boolean inplace = ((DynamicMetadataOptions) options).getBoolean(k + ".inPlace");
+    File cachedir = ((DynamicMetadataOptions) options).getFile(k + ".cacheDirectory");
+    if (elapsed == null || inplace == null) {
+      LOGGER.warn("config: memoizer options not found, reader will not be wrapped");
+      return r;
+    }
+    if (inplace) {
+      return new Memoizer(r, elapsed);
+    } else if (cachedir != null) {
+      return new Memoizer(r, elapsed, cachedir);
+    }
+    else {
+      return r;
+    }
+  }
 
   /**
    *  Returns whether the {@link #reader} instance currently active was loaded

components/formats-bsd/src/loci/formats/in/DicomReader.java

@@ -53,6 +53,8 @@
 import loci.formats.FormatException;
 import loci.formats.FormatReader;
 import loci.formats.FormatTools;
+import loci.formats.IFormatReader;
+import loci.formats.Memoizer;
 import loci.formats.MetadataTools;
 import loci.formats.UnsupportedCompressionException;
 import loci.formats.codec.Codec;
@@ -153,7 +155,7 @@ public class DicomReader extends FormatReader {
   private int originalSeries;
   private int originalX, originalY;
 
-  private DicomReader helper;
+  private IFormatReader helper;
 
   private List<String> companionFiles = new ArrayList<String>();
 
@@ -494,6 +496,7 @@ protected void initFile(String id) throws FormatException, IOException {
     attachCompanionFiles();
 
     helper = new DicomReader();
+    helper = Memoizer.wrap(getMetadataOptions(), helper);
     helper.setGroupFiles(false);
 
     m.littleEndian = true;

components/formats-bsd/src/loci/formats/in/MicromanagerReader.java

@@ -50,6 +50,8 @@
 import loci.formats.FormatException;
 import loci.formats.FormatReader;
 import loci.formats.FormatTools;
+import loci.formats.IFormatReader;
+import loci.formats.Memoizer;
 import loci.formats.MetadataTools;
 import loci.formats.meta.MetadataStore;
 import loci.formats.tiff.IFD;
@@ -99,7 +101,7 @@ public class MicromanagerReader extends FormatReader {
   // -- Fields --
 
   /** Helper reader for TIFF files. */
-  private MinimalTiffReader tiffReader;
+  private IFormatReader tiffReader;
 
   private Vector<Position> positions;
   private int start = 0;
@@ -260,6 +262,7 @@ public int getOptimalTileHeight() {
   public void initFile(String id) throws FormatException, IOException {
     super.initFile(id);
     tiffReader = new MinimalTiffReader();
+    tiffReader = Memoizer.wrap(getMetadataOptions(), tiffReader);
     positions = new Vector<Position>();
 
     LOGGER.info("Reading metadata file");

components/formats-bsd/src/loci/formats/in/NRRDReader.java

@@ -48,6 +48,7 @@
 import loci.formats.FormatTools;
 import loci.formats.IFormatReader;
 import loci.formats.ImageReader;
+import loci.formats.Memoizer;
 import loci.formats.MetadataTools;
 import loci.formats.UnknownFormatException;
 import loci.formats.UnsupportedCompressionException;
@@ -67,7 +68,7 @@ public class NRRDReader extends FormatReader {
   // -- Fields --
 
   /** Helper reader. */
-  private ImageReader helper;
+  private IFormatReader helper;
 
   /** Name of data file, if the current extension is 'nhdr'. */
   private String dataFile;
@@ -259,6 +260,7 @@ protected void initFile(String id) throws FormatException, IOException {
       }
     }
     helper = new ImageReader(newClasses);
+    helper = Memoizer.wrap(getMetadataOptions(), helper);
     helper.setMetadataOptions(
       new DefaultMetadataOptions(MetadataLevel.MINIMUM));
 

components/formats-bsd/src/loci/formats/in/OMETiffReader.java

@@ -53,6 +53,7 @@
 import loci.formats.FormatException;
 import loci.formats.FormatTools;
 import loci.formats.IFormatReader;
+import loci.formats.Memoizer;
 import loci.formats.MetadataTools;
 import loci.formats.MissingLibraryException;
 import loci.formats.Modulo;
@@ -548,6 +549,7 @@ protected void initFile(String id) throws FormatException, IOException {
 
     if (!isGroupFiles() && !isSingleFile(currentId)) {
       IFormatReader reader = new MinimalTiffReader();
+      reader = Memoizer.wrap(getMetadataOptions(), reader);
       initializeReader(reader, currentId);
       core.set(0, 0, new OMETiffCoreMetadata(reader.getCoreMetadataList().get(0)));
       int ifdCount = reader.getImageCount();
@@ -1021,6 +1023,7 @@ else if (t == 0) {
         }
         if (info[s][0].reader == null) {
           info[s][0].reader = new MinimalTiffReader();
+          info[s][0].reader = Memoizer.wrap(getMetadataOptions(), info[s][0].reader);
         }
         String firstFile = info[s][0].id;
         if (firstFile == null ||

components/formats-bsd/src/loci/formats/in/ZipReader.java

@@ -45,7 +45,9 @@
 import loci.formats.CoreMetadata;
 import loci.formats.FormatException;
 import loci.formats.FormatReader;
+import loci.formats.IFormatReader;
 import loci.formats.ImageReader;
+import loci.formats.Memoizer;
 
 /**
  * Reader for Zip files.
@@ -54,7 +56,7 @@ public class ZipReader extends FormatReader {
 
   // -- Fields --
 
-  private transient ImageReader reader;
+  private transient IFormatReader reader;
   private String entryName;
 
   private ArrayList<String> mappedFiles = new ArrayList<String>();
@@ -125,6 +127,7 @@ public void reopenFile() throws IOException {
     }
     else {
       reader = new ImageReader();
+      reader = Memoizer.wrap(getMetadataOptions(), reader);
     }
     findZipEntries();
   }
@@ -139,6 +142,7 @@ protected void initFile(String id) throws FormatException, IOException {
       reader.close();
     }
     reader = new ImageReader();
+    reader = Memoizer.wrap(getMetadataOptions(), reader);
 
     reader.setMetadataOptions(getMetadataOptions());
     reader.setMetadataFiltered(isMetadataFiltered());

components/formats-gpl/src/loci/formats/in/BDReader.java

@@ -48,6 +48,8 @@
 import loci.formats.FormatException;
 import loci.formats.FormatReader;
 import loci.formats.FormatTools;
+import loci.formats.IFormatReader;
+import loci.formats.Memoizer;
 import loci.formats.MetadataTools;
 import loci.formats.meta.MetadataStore;
 import loci.formats.tiff.IFD;
@@ -81,7 +83,7 @@ public class BDReader extends FormatReader {
   private List<String> wellLabels = new ArrayList<String>();
   private String plateName, plateDescription;
   private String[][] tiffs;
-  private MinimalTiffReader reader;
+  private IFormatReader reader;
 
   private String roiFile;
   private double[] emWave, exWave;
@@ -344,6 +346,7 @@ protected void initFile(String id) throws FormatException, IOException {
     tiffs = getTiffs();
 
     reader = new MinimalTiffReader();
+    reader = Memoizer.wrap(getMetadataOptions(), reader);
     reader.setId(tiffs[0][0]);
 
     int sizeX = reader.getSizeX();

components/formats-gpl/src/loci/formats/in/CV7000Reader.java

@@ -42,6 +42,8 @@
 import loci.formats.FormatException;
 import loci.formats.FormatReader;
 import loci.formats.FormatTools;
+import loci.formats.IFormatReader;
+import loci.formats.Memoizer;
 import loci.formats.MetadataTools;
 import loci.formats.meta.MetadataStore;
 import loci.formats.tiff.IFD;
@@ -79,7 +81,7 @@ public class CV7000Reader extends FormatReader {
 
   private String[] allFiles;
   private Location parent;
-  private MinimalTiffReader reader;
+  private IFormatReader reader;
   private String wppPath;
   private String detailPath;
   private String measurementPath;
@@ -334,6 +336,7 @@ protected void initFile(String id) throws FormatException, IOException {
     }
 
     reader = new MinimalTiffReader();
+    reader = Memoizer.wrap(getMetadataOptions(), reader);
     reader.setId(firstFile);
     core.clear();
     core.add(new CoreMetadata(reader.getCoreMetadataList().get(0)));

components/formats-gpl/src/loci/formats/in/CellSensReader.java

@@ -42,6 +42,7 @@
 import loci.formats.FormatReader;
 import loci.formats.FormatTools;
 import loci.formats.IFormatReader;
+import loci.formats.Memoizer;
 import loci.formats.MetadataTools;
 import loci.formats.codec.Codec;
 import loci.formats.codec.CodecOptions;
@@ -1076,12 +1077,13 @@ else if (dim.equals("T")) {
         case PNG:
           file = "tile.png";
           reader = new APNGReader();
+          reader = Memoizer.wrap(getMetadataOptions(), reader);
         case BMP:
           if (reader == null) {
             file = "tile.bmp";
             reader = new BMPReader();
+            reader = Memoizer.wrap(getMetadataOptions(), reader);
           }
-
           byte[] b = new byte[(int) (end - offset)];
           ets.read(b);
           Location.mapFile(file, new ByteArrayHandle(b));

components/formats-gpl/src/loci/formats/in/CellVoyagerReader.java

@@ -44,6 +44,8 @@
 import loci.formats.FormatException;
 import loci.formats.FormatReader;
 import loci.formats.FormatTools;
+import loci.formats.IFormatReader;
+import loci.formats.Memoizer;
 import loci.formats.MetadataTools;
 import loci.formats.meta.MetadataStore;
 import loci.formats.ome.OMEXMLMetadata;
@@ -146,7 +148,7 @@ public byte[] openBytes( final int no, final byte[] buf, final int x, final int
     final int areaIndex = indices[ 1 ];
     final WellInfo well = wells.get( wellIndex );
     final AreaInfo area = well.areas.get( areaIndex );
-    final MinimalTiffReader tiffReader = new MinimalTiffReader();
+    final IFormatReader tiffReader = Memoizer.wrap(getMetadataOptions(), new MinimalTiffReader());
 
     imageFolder = new Location(currentId).getAbsoluteFile().getParentFile();
     imageFolder = new Location(imageFolder, "Image");

components/formats-gpl/src/loci/formats/in/CellWorxReader.java

@@ -43,6 +43,7 @@
 import loci.formats.FormatReader;
 import loci.formats.FormatTools;
 import loci.formats.IFormatReader;
+import loci.formats.Memoizer;
 import loci.formats.MetadataTools;
 import loci.formats.meta.IMetadata;
 import loci.formats.meta.MetadataStore;
@@ -856,6 +857,7 @@ protected IFormatReader getReader(String file, boolean omexml)
     throws FormatException, IOException
   {
     IFormatReader pnl = new DeltavisionReader();
+    pnl = Memoizer.wrap(getMetadataOptions(), pnl);
     initReader(pnl, file, omexml);
     return pnl;
   }

components/formats-gpl/src/loci/formats/in/ColumbusReader.java

@@ -43,6 +43,8 @@
 import loci.formats.FormatException;
 import loci.formats.FormatReader;
 import loci.formats.FormatTools;
+import loci.formats.IFormatReader;
+import loci.formats.Memoizer;
 import loci.formats.MetadataTools;
 import loci.formats.meta.MetadataStore;
 
@@ -80,7 +82,7 @@ public class ColumbusReader extends FormatReader {
 
   private ArrayList<String> metadataFiles = new ArrayList<String>();
   private ArrayList<Plane> planes = new ArrayList<Plane>();
-  private MinimalTiffReader reader;
+  private IFormatReader reader;
 
   private int nFields = 0;
   private String acquisitionDate;
@@ -296,6 +298,7 @@ public int compare(Plane p1, Plane p2) {
     planes.clear();
 
     reader = new MinimalTiffReader();
+    reader = Memoizer.wrap(getMetadataOptions(), reader);
     reader.setId(tmpPlanes[0].file);
     core = reader.getCoreMetadataList();
 

components/formats-gpl/src/loci/formats/in/HamamatsuVMSReader.java

@@ -43,6 +43,8 @@
 import loci.formats.FormatException;
 import loci.formats.FormatReader;
 import loci.formats.FormatTools;
+import loci.formats.IFormatReader;
+import loci.formats.Memoizer;
 import loci.formats.MetadataTools;
 import loci.formats.codec.JPEGTileDecoder;
 import loci.formats.meta.MetadataStore;
@@ -148,7 +150,8 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
     }
 
     if (getSizeX() <= MAX_SIZE || getSizeY() <= MAX_SIZE) {
-      JPEGReader reader = new JPEGReader();
+      IFormatReader reader = new JPEGReader();
+      reader = Memoizer.wrap(getMetadataOptions(), reader);
       reader.setId(file);
       reader.openBytes(0, buf, x, y, w, h);
       reader.close();