Merge pull request #29 from chris-allan/fix-uint16-padding

Fix issues with uint16 tile padding on the East and South edges
glencoesoftware · May 20, 2020 · edc3619 · edc3619
2 parents f26b41d + 1e4dc7d
commit edc3619
Show file tree

Hide file tree

Showing 2 changed files with 78 additions and 4 deletions.
diff --git a/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java b/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java
@@ -666,7 +666,7 @@ private void convertPyramid(PyramidSeries s)
     }
 
     int rgbChannels = s.rgb ? s.c : 1;
-
+    int bytesPerPixel = FormatTools.getBytesPerPixel(s.pixelType);
     try {
       for (int resolution=0; resolution<s.numberOfResolutions; resolution++) {
         LOG.info("Converting resolution #{}", resolution);
@@ -718,12 +718,14 @@ private void convertPyramid(PyramidSeries s)
                       else {
                         // padded tile, use descriptor X and Y tile size
                         byte[] realTile =
-                          new byte[descriptor.tileSizeX * descriptor.tileSizeY];
+                          new byte[descriptor.tileSizeX * descriptor.tileSizeY
+                                   * bytesPerPixel];
                         int totalRows = region.height;
-                        int inRowLen = tileBytes.length / totalRows;
+                        int inRowLen = region.width * bytesPerPixel;
+                        int outRowLen = descriptor.tileSizeX * bytesPerPixel;
                         for (int row=0; row<totalRows; row++) {
                           System.arraycopy(tileBytes, row * inRowLen,
-                            realTile, row * descriptor.tileSizeX, inRowLen);
+                            realTile, row * outRowLen, inRowLen);
                         }
                         writeTile(s, currentPlane, realTile,
                           currentIndex, currentResolution);

diff --git a/src/test/java/com/glencoesoftware/raw2ometiff/test/ConversionTest.java b/src/test/java/com/glencoesoftware/raw2ometiff/test/ConversionTest.java
@@ -9,6 +9,8 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.nio.ByteBuffer;
+import java.nio.ShortBuffer;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -21,6 +23,8 @@
 import com.glencoesoftware.pyramid.PyramidFromDirectoryWriter;
 
 import loci.formats.ImageReader;
+import loci.formats.tiff.IFDList;
+import loci.formats.tiff.TiffParser;
 import picocli.CommandLine;
 
 import org.junit.Assert;
@@ -190,4 +194,72 @@ public void testDefaults() throws Exception {
     }
   }
 
+  /**
+   * Test South and East edge padding.
+   */
+  @Test
+  public void testSouthEastEdgePadding() throws Exception {
+    input = fake();
+    assertBioFormats2Raw("-w", "240", "-h", "240");
+    assertTool("--compression", "raw");
+    try (ImageReader reader = new ImageReader()) {
+      reader.setFlattenedResolutions(false);
+      reader.setId(outputOmeTiff.toString());
+      Assert.assertEquals(2, reader.getResolutionCount());
+      Assert.assertEquals(240, reader.getOptimalTileWidth());
+      Assert.assertEquals(240, reader.getOptimalTileHeight());
+      ByteBuffer plane = ByteBuffer.wrap(reader.openBytes(0));
+      Assert.assertEquals(512 * 512, plane.capacity());
+      int offset = 0;
+      for (int y = 0; y < reader.getSizeY(); y++) {
+        offset = (y * 512) + 511;
+        Assert.assertEquals(255, Byte.toUnsignedInt(plane.get(offset)));
+      }
+    }
+    try (TiffParser tiffParser = new TiffParser(outputOmeTiff.toString())) {
+      IFDList mainIFDs = tiffParser.getMainIFDs();
+      Assert.assertEquals(1, mainIFDs.size());
+      int tileSize = 240 * 240;
+      Assert.assertArrayEquals(new long[] {
+        tileSize, tileSize, tileSize,  // Row 1
+        tileSize, tileSize, tileSize,  // Row 2
+        tileSize, tileSize, tileSize   // Row 3
+      }, mainIFDs.get(0).getStripByteCounts());
+    }
+  }
+
+  /**
+   * Test edge padding uint16.
+   */
+  @Test
+  public void testEdgePaddingUint16() throws Exception {
+    input = fake("pixelType", "uint16");
+    assertBioFormats2Raw("-w", "240", "-h", "240");
+    assertTool("--compression", "raw");
+    try (ImageReader reader = new ImageReader()) {
+      reader.setFlattenedResolutions(false);
+      reader.setId(outputOmeTiff.toString());
+      Assert.assertEquals(2, reader.getResolutionCount());
+      Assert.assertEquals(240, reader.getOptimalTileWidth());
+      Assert.assertEquals(240, reader.getOptimalTileHeight());
+      ShortBuffer plane = ByteBuffer.wrap(reader.openBytes(0)).asShortBuffer();
+      Assert.assertEquals(512 * 512, plane.capacity());
+      int offset = 0;
+      for (int y = 0; y < reader.getSizeY(); y++) {
+        offset = (y * 512) + 511;
+        Assert.assertEquals(511, Short.toUnsignedInt(plane.get(offset)));
+      }
+    }
+    try (TiffParser tiffParser = new TiffParser(outputOmeTiff.toString())) {
+      IFDList mainIFDs = tiffParser.getMainIFDs();
+      Assert.assertEquals(1, mainIFDs.size());
+      int tileSize = 240 * 240 * 2;
+      Assert.assertArrayEquals(new long[] {
+        tileSize, tileSize, tileSize,  // Row 1
+        tileSize, tileSize, tileSize,  // Row 2
+        tileSize, tileSize, tileSize   // Row 3
+      }, mainIFDs.get(0).getStripByteCounts());
+    }
+  }
+
 }