Extend precompressed tile writing to OME-TIFF

Mostly this reuses logic in the basic TIFF writer.
melissalinkert · May 1, 2024 · 92ec581 · 92ec581
1 parent 3146c90
commit 92ec581
Show file tree

Hide file tree

Showing 3 changed files with 42 additions and 7 deletions.
diff --git a/components/formats-bsd/src/loci/formats/out/OMETiffWriter.java b/components/formats-bsd/src/loci/formats/out/OMETiffWriter.java
@@ -199,6 +199,24 @@ public void close() throws IOException {
 
   // -- IFormatWriter API methods --
 
+  @Override
+  public void saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)
+    throws FormatException, IOException
+  {
+    super.saveCompressedBytes(no, buf, x, y, w, h);
+
+    int index = no;
+    while (imageLocations[series][index] != null) {
+      if (index < imageLocations[series].length - 1) {
+        index++;
+      }
+      else {
+        break;
+      }
+    }
+    imageLocations[series][index] = currentId;
+  }
+
   /**
    * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int)
    */

diff --git a/components/formats-bsd/src/loci/formats/out/PyramidOMETiffWriter.java b/components/formats-bsd/src/loci/formats/out/PyramidOMETiffWriter.java
@@ -70,6 +70,19 @@ public boolean isThisType(String name) {
 
   // -- IFormatWriter API methods --
 
+  protected IFD makeIFD() throws FormatException, IOException {
+    IFD ifd = super.makeIFD();
+    if (getResolution() > 0) {
+      ifd.put(IFD.NEW_SUBFILE_TYPE, 1);
+    }
+    else {
+      if (!ifd.containsKey(IFD.SUB_IFD)) {
+        ifd.put(IFD.SUB_IFD, (long) 0);
+      }
+    }
+    return ifd;
+  }
+
   @Override
   public void saveBytes(int no, byte[] buf, IFD ifd, int x, int y, int w, int h)
     throws FormatException, IOException

diff --git a/components/formats-bsd/src/loci/formats/out/TiffWriter.java b/components/formats-bsd/src/loci/formats/out/TiffWriter.java
@@ -178,7 +178,7 @@ public void saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)
     LOGGER.warn("saveCompressedBytes(series={}, resolution={}, no={}, x={}, y={})",
       series, resolution, no, x, y);
 
-    IFD ifd = new IFD();
+    IFD ifd = makeIFD();
     MetadataRetrieve retrieve = getMetadataRetrieve();
     int type = FormatTools.pixelTypeFromString(
         retrieve.getPixelsType(series).toString());
@@ -193,12 +193,6 @@ public void saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)
       throw new IllegalArgumentException("Compressed tile dimensions must match tile size");
     }
 
-    boolean usingTiling = currentTileSizeX > 0 && currentTileSizeY > 0;
-    if (usingTiling) {
-      ifd.put(new Integer(IFD.TILE_WIDTH), new Long(currentTileSizeX));
-      ifd.put(new Integer(IFD.TILE_LENGTH), new Long(currentTileSizeY));
-    }
-
     // This operation is synchronized
     synchronized (this) {
       // This operation is synchronized against the TIFF saver.
@@ -221,6 +215,16 @@ public void saveCompressedBytes(int no, byte[] buf, int x, int y, int w, int h)
       nChannels, lastPlane && lastSeries && lastResolution, x, y);
   }
 
+  protected IFD makeIFD() throws FormatException, IOException {
+    IFD ifd = new IFD();
+    boolean usingTiling = getTileSizeX() > 0 && getTileSizeY() > 0;
+    if (usingTiling) {
+      ifd.put(new Integer(IFD.TILE_WIDTH), new Long(getTileSizeX()));
+      ifd.put(new Integer(IFD.TILE_LENGTH), new Long(getTileSizeY()));
+    }
+    return ifd;
+  }
+
   // -- FormatWriter API methods --
 
   /* @see loci.formats.FormatWriter#setId(String) */