Refactor generic TIFF tile logic

melissalinkert · Apr 9, 2024 · e21ed51 · e21ed51
1 parent 41eb29e
commit e21ed51
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Showing 3 changed files with 74 additions and 74 deletions.
diff --git a/components/formats-bsd/src/loci/formats/in/MinimalTiffReader.java b/components/formats-bsd/src/loci/formats/in/MinimalTiffReader.java
@@ -705,4 +705,73 @@ protected void initTiffParser() {
     tiffParser.setUse64BitOffsets(use64Bit);
   }
 
+  /**
+   * Get the index of the tile corresponding to given IFD (plane)
+   * and tile XY indexes.
+   *
+   * @param ifd IFD for the requested tile's plane
+   * @param x tile X index
+   * @param y tile Y index
+   * @return corresponding tile index
+   */
+  protected int getTileIndex(IFD ifd, int x, int y) throws FormatException {
+    int rows = (int) ifd.getTilesPerColumn();
+    int cols = (int) ifd.getTilesPerRow();
+
+    if (x < 0 || x >= cols) {
+      throw new IllegalArgumentException("X index " + x + " not in range [0, " + cols + ")");
+    }
+    if (y < 0 || y >= rows) {
+      throw new IllegalArgumentException("Y index " + y + " not in range [0, " + rows + ")");
+    }
+
+    return (cols * y) + x;
+  }
+
+  protected long getCompressedByteCount(IFD ifd, int x, int y) throws FormatException, IOException {
+    long[] byteCounts = ifd.getStripByteCounts();
+    int tileIndex = getTileIndex(ifd, x, y);
+    byte[] jpegTable = (byte[]) ifd.getIFDValue(IFD.JPEG_TABLES);
+    int jpegTableBytes = jpegTable == null ? 0 : jpegTable.length - 2;
+    long expectedBytes = byteCounts[tileIndex];
+    if (expectedBytes > 0) {
+      expectedBytes += jpegTableBytes;
+    }
+    if (expectedBytes < 0 || expectedBytes > Integer.MAX_VALUE) {
+      throw new IOException("Invalid compressed tile size: " + expectedBytes);
+    }
+    return expectedBytes;
+  }
+
+  protected byte[] copyTile(IFD ifd, byte[] buf, int x, int y) throws FormatException, IOException {
+    long[] offsets = ifd.getStripOffsets();
+    long[] byteCounts = ifd.getStripByteCounts();
+
+    int tileIndex = getTileIndex(ifd, x, y);
+
+    byte[] jpegTable = (byte[]) ifd.getIFDValue(IFD.JPEG_TABLES);
+    int jpegTableBytes = jpegTable == null ? 0 : jpegTable.length - 2;
+    long expectedBytes = getCompressedByteCount(ifd, x, y);
+
+    if (buf.length < expectedBytes) {
+      throw new IllegalArgumentException("Tile buffer too small: expected >=" +
+        expectedBytes + ", got " + buf.length);
+    }
+    else if (expectedBytes < 0 || expectedBytes > Integer.MAX_VALUE) {
+      throw new IOException("Invalid compressed tile size: " + expectedBytes);
+    }
+
+    if (jpegTable != null && expectedBytes > 0) {
+      System.arraycopy(jpegTable, 0, buf, 0, jpegTable.length - 2);
+      // skip over the duplicate SOI marker
+      tiffParser.getStream().seek(offsets[tileIndex] + 2);
+      tiffParser.getStream().readFully(buf, jpegTable.length - 2, (int) byteCounts[tileIndex]);
+    }
+    else if (byteCounts[tileIndex] > 0) {
+      tiffParser.getStream().seek(offsets[tileIndex]);
+      tiffParser.getStream().readFully(buf, 0, (int) byteCounts[tileIndex]);
+    }
+    return buf;
+  }
+
 }
diff --git a/components/formats-gpl/src/loci/formats/in/NDPIReader.java b/components/formats-gpl/src/loci/formats/in/NDPIReader.java
@@ -149,8 +149,8 @@ public byte[] openCompressedBytes(int no, int x, int y) throws FormatException,
     IFD ifd = ifds.get(ifdIndex);
 
     if (useTiffParser(ifd)) {
-      // TODO
-      return null;
+      byte[] buf = new byte[(int) getCompressedByteCount(ifd, x, y)];
+      return openCompressedBytes(no, buf, x, y);
     }
 
     if (initializedSeries != getCoreIndex() || initializedPlane != no) {
@@ -169,8 +169,7 @@ public byte[] openCompressedBytes(int no, byte[] buf, int x, int y) throws Forma
     IFD ifd = ifds.get(ifdIndex);
 
     if (useTiffParser(ifd)) {
-      // TODO
-      return buf;
+      return copyTile(ifd, buf, x, y);
     }
 
     if (initializedSeries != getCoreIndex() || initializedPlane != no) {

diff --git a/components/formats-gpl/src/loci/formats/in/SVSReader.java b/components/formats-gpl/src/loci/formats/in/SVSReader.java
@@ -306,60 +306,15 @@ public int getTileColumns(int no) {
   public byte[] openCompressedBytes(int no, int x, int y) throws FormatException, IOException {
     FormatTools.assertId(currentId, true, 1);
     IFD ifd = getIFD(no);
-    long[] byteCounts = ifd.getStripByteCounts();
-    int tileIndex = getTileIndex(ifd, x, y);
-
-    byte[] jpegTable = (byte[]) ifd.getIFDValue(IFD.JPEG_TABLES);
-    int jpegTableBytes = jpegTable == null ? 0 : jpegTable.length - 2;
-    long expectedBytes = byteCounts[tileIndex];
-    if (expectedBytes > 0) {
-      expectedBytes += jpegTableBytes;
-    }
-
-    if (expectedBytes < 0 || expectedBytes > Integer.MAX_VALUE) {
-      throw new IOException("Invalid compressed tile size: " + expectedBytes);
-    }
-
-    byte[] buf = new byte[(int) expectedBytes];
+    byte[] buf = new byte[(int) getCompressedByteCount(ifd, x, y)];
     return openCompressedBytes(no, buf, x, y);
   }
 
   @Override
   public byte[] openCompressedBytes(int no, byte[] buf, int x, int y) throws FormatException, IOException {
     FormatTools.assertId(currentId, true, 1);
     IFD ifd = getIFD(no);
-    long[] offsets = ifd.getStripOffsets();
-    long[] byteCounts = ifd.getStripByteCounts();
-
-    int tileIndex = getTileIndex(ifd, x, y);
-
-    byte[] jpegTable = (byte[]) ifd.getIFDValue(IFD.JPEG_TABLES);
-    int jpegTableBytes = jpegTable == null ? 0 : jpegTable.length - 2;
-    long expectedBytes = byteCounts[tileIndex];
-    if (expectedBytes > 0) {
-      expectedBytes += jpegTableBytes;
-    }
-
-    if (buf.length < expectedBytes) {
-      throw new IllegalArgumentException("Tile buffer too small: expected >=" +
-        expectedBytes + ", got " + buf.length);
-    }
-    else if (expectedBytes < 0 || expectedBytes > Integer.MAX_VALUE) {
-      throw new IOException("Invalid compressed tile size: " + expectedBytes);
-    }
-
-    if (jpegTable != null && expectedBytes > 0) {
-      System.arraycopy(jpegTable, 0, buf, 0, jpegTable.length - 2);
-      // skip over the duplicate SOI marker
-      tiffParser.getStream().seek(offsets[tileIndex] + 2);
-      tiffParser.getStream().readFully(buf, jpegTable.length - 2, (int) byteCounts[tileIndex]);
-    }
-    else if (byteCounts[tileIndex] > 0) {
-      tiffParser.getStream().seek(offsets[tileIndex]);
-      tiffParser.getStream().readFully(buf, 0, (int) byteCounts[tileIndex]);
-    }
-
-    return buf;
+    return copyTile(ifd, buf, x, y);
   }
 
   @Override
@@ -873,27 +828,4 @@ protected IFD getIFD(int no) {
     return ifds.get(ifd);
   }
 
-  /**
-   * Get the index of the tile corresponding to given IFD (plane)
-   * and tile XY indexes.
-   *
-   * @param ifd IFD for the requested tile's plane
-   * @param x tile X index
-   * @param y tile Y index
-   * @return corresponding tile index
-   */
-  protected int getTileIndex(IFD ifd, int x, int y) throws FormatException {
-    int rows = (int) ifd.getTilesPerColumn();
-    int cols = (int) ifd.getTilesPerRow();
-
-    if (x < 0 || x >= cols) {
-      throw new IllegalArgumentException("X index " + x + " not in range [0, " + cols + ")");
-    }
-    if (y < 0 || y >= rows) {
-      throw new IllegalArgumentException("Y index " + y + " not in range [0, " + rows + ")");
-    }
-
-    return (cols * y) + x;
-  }
-
 }