Merge branch 'develop' of github.com:openmicroscopy/bioformats into d…

…icom-reader-precompressed
ome · Aug 8, 2024 · 00ac6cc · 00ac6cc
2 parents 93e38d8 + 0a895ae
commit 00ac6cc
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Showing 14 changed files with 557 additions and 197 deletions.
diff --git a/components/bio-formats-tools/src/loci/formats/tools/ImageConverter.java b/components/bio-formats-tools/src/loci/formats/tools/ImageConverter.java
@@ -1270,7 +1270,14 @@ private boolean doTileConversion(IFormatWriter writer, String outputFile)
   {
     MetadataStore r = reader.getMetadataStore();
     if ((r instanceof IPyramidStore) && ((IPyramidStore) r).getResolutionCount(reader.getSeries()) > 1) {
-      return true;
+      // if we asked to try a precompressed conversion,
+      // then the writer's tile sizes will have been set automatically
+      // according to the input data
+      // the conversion must then be performed tile-wise to match the tile sizes,
+      // even if precompression doesn't end up being possible
+      if (precompressed) {
+        return true;
+      }
     }
     return DataTools.safeMultiply64(width, height) >= DataTools.safeMultiply64(4096, 4096) ||
       saveTileWidth > 0 || saveTileHeight > 0;

diff --git a/components/formats-bsd/src/loci/formats/gui/PreviewPane.java b/components/formats-bsd/src/loci/formats/gui/PreviewPane.java
@@ -215,7 +215,9 @@ public void run() {
 
       try { // catch-all for unanticipated exceptions
         final String id = loadId;
-        if (id == lastId) continue;
+        if ((id == null && lastId == null) || (id != null && id.equals(lastId))) {
+          continue;
+        }
         if (id != null && lastId != null) {
           String[] files = reader.getUsedFiles();
           boolean found = false;
@@ -260,7 +262,7 @@ public void run() {
           lastId = null;
           continue;
         }
-        if (id != loadId) {
+        if (!id.equals(loadId)) {
           SwingUtilities.invokeLater(refresher);
           continue;
         }

diff --git a/components/formats-bsd/src/loci/formats/in/ICSReader.java b/components/formats-bsd/src/loci/formats/in/ICSReader.java
@@ -1479,10 +1479,12 @@ else if (labels.equalsIgnoreCase("x y t")) {
     MetadataTools.populatePixels(store, this, true);
 
     // populate Image data
-    imageName = imageName.replace('/', File.separatorChar);
-    imageName = imageName.replace('\\', File.separatorChar);
-    imageName = imageName.substring(imageName.lastIndexOf(File.separator) + 1);
-    store.setImageName(imageName, 0);
+    if (imageName != null) {
+      imageName = imageName.replace('/', File.separatorChar);
+      imageName = imageName.replace('\\', File.separatorChar);
+      imageName = imageName.substring(imageName.lastIndexOf(File.separator) + 1);
+      store.setImageName(imageName, 0);
+    }
 
     if (date != null) store.setImageAcquisitionDate(new Timestamp(date), 0);
 

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-bsd/src/loci/formats/in/OMEXMLReader.java b/components/formats-bsd/src/loci/formats/in/OMEXMLReader.java
@@ -290,7 +290,7 @@ protected void initFile(String id) throws FormatException, IOException {
       Integer t = omexmlMeta.getPixelsSizeT(i).getValue();
       Integer z = omexmlMeta.getPixelsSizeZ(i).getValue();
       Integer c = omexmlMeta.getPixelsSizeC(i).getValue();
-      if (w == null || h == null || t == null || z == null | c == null) {
+      if (w == null || h == null || t == null || z == null || c == null) {
         throw new FormatException("Image dimensions not found");
       }