Merge pull request glencoesoftware#31 from chris-allan/f32-f64-pix

Add support for float and double pixel types
joshmoore · Apr 22, 2020 · 9968023 · 9968023
2 parents 0fd59e3 + 4f8bac0
commit 9968023
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Showing 3 changed files with 83 additions and 11 deletions.
diff --git a/config/checkstyle/checkstyle.xml b/config/checkstyle/checkstyle.xml
@@ -131,7 +131,9 @@
 
         <!-- Checks for blocks. You know, those {}'s         -->
         <!-- See https://checkstyle.org/config_blocks.html -->
-        <module name="AvoidNestedBlocks"/>
+        <module name="AvoidNestedBlocks">
+            <property name="allowInSwitchCase" value="true"/>
+        </module>
         <module name="EmptyBlock"/>
         <module name="LeftCurly">
             <property name="option" value="nlow"/>

diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
@@ -51,6 +51,8 @@
 import org.janelia.saalfeldlab.n5.DataBlock;
 import org.janelia.saalfeldlab.n5.DataType;
 import org.janelia.saalfeldlab.n5.DatasetAttributes;
+import org.janelia.saalfeldlab.n5.DoubleArrayDataBlock;
+import org.janelia.saalfeldlab.n5.FloatArrayDataBlock;
 import org.janelia.saalfeldlab.n5.GzipCompression;
 import org.janelia.saalfeldlab.n5.Lz4Compression;
 import org.janelia.saalfeldlab.n5.N5FSReader;
@@ -713,23 +715,38 @@ private void processTile(
         return;
       }
 
-      int bytesPerPixel = FormatTools.getBytesPerPixel(pixelType);
-      switch (bytesPerPixel) {
-        case 1:
+      ByteBuffer bb = ByteBuffer.wrap(tile);
+      if (resolution == 0 && isLittleEndian) {
+        bb = bb.order(ByteOrder.LITTLE_ENDIAN);
+      }
+      switch (pixelType) {
+        case FormatTools.INT8:
+        case FormatTools.UINT8: {
           dataBlock = new ByteArrayDataBlock(size, gridPosition, tile);
           break;
-        case 2:
+        }
+        case FormatTools.INT16:
+        case FormatTools.UINT16: {
           short[] asShort = new short[tile.length / 2];
-          ByteBuffer bb = ByteBuffer.wrap(tile);
-          if (resolution == 0 && isLittleEndian) {
-            bb = bb.order(ByteOrder.LITTLE_ENDIAN);
-          }
           bb.asShortBuffer().get(asShort);
           dataBlock = new ShortArrayDataBlock(size, gridPosition, asShort);
           break;
+        }
+        case FormatTools.FLOAT: {
+          float[] asFloat = new float[tile.length / 4];
+          bb.asFloatBuffer().get(asFloat);
+          dataBlock = new FloatArrayDataBlock(size, gridPosition, asFloat);
+          break;
+        }
+        case FormatTools.DOUBLE: {
+          double[] asDouble = new double[tile.length / 8];
+          bb.asDoubleBuffer().get(asDouble);
+          dataBlock = new DoubleArrayDataBlock(size, gridPosition, asDouble);
+          break;
+        }
         default:
-          throw new FormatException(
-              "Unsupported bytes per pixel: " + bytesPerPixel);
+          throw new FormatException("Unsupported pixel type: "
+              + FormatTools.getPixelTypeString(pixelType));
       }
     }
     finally {
@@ -817,6 +834,12 @@ public void saveResolutions(int series)
       case FormatTools.UINT16:
         dataType = DataType.UINT16;
         break;
+      case FormatTools.FLOAT:
+        dataType = DataType.FLOAT32;
+        break;
+      case FormatTools.DOUBLE:
+        dataType = DataType.FLOAT64;
+        break;
       default:
         throw new FormatException("Unsupported pixel type: "
             + FormatTools.getPixelTypeString(pixelType));

diff --git a/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java b/src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
@@ -24,6 +24,7 @@
 import loci.formats.in.FakeReader;
 import picocli.CommandLine;
 
+import org.janelia.saalfeldlab.n5.DataType;
 import org.janelia.saalfeldlab.n5.DatasetAttributes;
 import org.janelia.saalfeldlab.n5.zarr.N5ZarrReader;
 import org.junit.Assert;
@@ -371,4 +372,50 @@ public void testMultiT() throws Exception {
     Assert.assertArrayEquals(new int[] {0, 1, 0, 0, 1}, seriesPlaneNumberZCT);
   }
 
+  /**
+   * Test float pixel type.
+   */
+  @Test
+  public void testFloatPixelType() throws Exception {
+    input = fake("pixelType", "float");
+    assertTool();
+    N5ZarrReader z =
+            new N5ZarrReader(output.resolve("data.zarr").toString());
+
+    // Check series dimensions and special pixels
+    DatasetAttributes da = z.getDatasetAttributes("/0/0");
+    Assert.assertEquals(DataType.FLOAT32, da.getDataType());
+    Assert.assertArrayEquals(
+        new long[] {512, 512, 1, 1, 1}, da.getDimensions());
+    Assert.assertArrayEquals(
+        new int[] {512, 512, 1, 1, 1}, da.getBlockSize());
+    ByteBuffer tile = z.readBlock("/0/0", da, new long[] {0, 0, 0, 0, 0})
+        .toByteBuffer();
+    int[] seriesPlaneNumberZCT = FakeReader.readSpecialPixels(tile.array());
+    Assert.assertArrayEquals(new int[] {0, 0, 0, 0, 0}, seriesPlaneNumberZCT);
+  }
+
+  /**
+   * Test double pixel type.
+   */
+  @Test
+  public void testDoublePixelType() throws Exception {
+    input = fake("pixelType", "double");
+    assertTool();
+    N5ZarrReader z =
+            new N5ZarrReader(output.resolve("data.zarr").toString());
+
+    // Check series dimensions and special pixels
+    DatasetAttributes da = z.getDatasetAttributes("/0/0");
+    Assert.assertEquals(DataType.FLOAT64, da.getDataType());
+    Assert.assertArrayEquals(
+        new long[] {512, 512, 1, 1, 1}, da.getDimensions());
+    Assert.assertArrayEquals(
+        new int[] {512, 512, 1, 1, 1}, da.getBlockSize());
+    ByteBuffer tile = z.readBlock("/0/0", da, new long[] {0, 0, 0, 0, 0})
+        .toByteBuffer();
+    int[] seriesPlaneNumberZCT = FakeReader.readSpecialPixels(tile.array());
+    Assert.assertArrayEquals(new int[] {0, 0, 0, 0, 0}, seriesPlaneNumberZCT);
+  }
+
 }