Imaris Reader: support for LZ4 compression and performance improvements

ant/java.xml

@@ -220,6 +220,30 @@ your FindBugs installation's lib directory. E.g.:
       <path refid="runtime.classpath"/>
     </unzip>
 
+    <!-- Merge ucar.nc2.filter.FilterProvider files -->
+    <pathconvert property="runtimePaths.string" refid="runtime.classpath" pathsep="${line.separator}"/>
+    <echo file="${build.dir}/unzip/runtimePaths.txt">${runtimePaths.string}</echo>
+    <loadfile property="cdmcorePath" srcFile="${build.dir}/unzip/runtimePaths.txt">
+      <filterchain>
+        <linecontains>
+          <contains value="cdm-core"/>
+        </linecontains>
+        <striplinebreaks/>
+      </filterchain>
+    </loadfile>
+    <loadfile property="formatsgplPath" srcFile="${build.dir}/unzip/runtimePaths.txt">
+      <filterchain>
+        <linecontains>
+          <contains value="formats-gpl"/>
+        </linecontains>
+        <striplinebreaks/>
+      </filterchain>
+    </loadfile>
+    <concat destfile="${build.dir}/unzip/META-INF/services/ucar.nc2.filter.FilterProvider" fixlastline="yes">
+      <zipentry zipfile="${cdmcorePath}" name="META-INF/services/ucar.nc2.filter.FilterProvider"/>
+      <zipentry zipfile="${formatsgplPath}" name="META-INF/services/ucar.nc2.filter.FilterProvider"/>
+    </concat>
+
     <jar destfile="${artifact.dir}/${bundle.jar}" filesetmanifest="skip">
       <zipfileset dir="${build.dir}/unzip"/>
       <manifest>

components/bundles/bioformats_package/assembly.xml

@@ -36,4 +36,9 @@
       <useProjectArtifact>false</useProjectArtifact>
     </dependencySet>
   </dependencySets>
+  <containerDescriptorHandlers>
+    <containerDescriptorHandler>
+      <handlerName>metaInf-services</handlerName>
+    </containerDescriptorHandler>
+  </containerDescriptorHandlers>
 </assembly>

components/formats-gpl/build.properties

@@ -14,7 +14,8 @@ component.deprecation    = true
 
 component.resources-bin  = loci/formats/bio-formats-logo.png \
                            loci/formats/utests/2008-09.ome \
-                           lib/**/*.dll
+                           lib/**/*.dll \
+                           META-INF/services/ucar.nc2.filter.FilterProvider
 component.resources-text =
 
 component.main-class     = loci.formats.gui.ImageViewer

components/formats-gpl/pom.xml

@@ -120,6 +120,11 @@
       <artifactId>kryo</artifactId>
       <version>${kryo.version}</version>
     </dependency>
+    <dependency>
+      <groupId>io.airlift</groupId>
+      <artifactId>aircompressor</artifactId>
+      <version>0.27</version>
+    </dependency>
 
     <!-- NB: dependency:analyze has false warning about xml-apis:xml-apis. -->
 

components/formats-gpl/src/META-INF/services/ucar.nc2.filter.FilterProvider

@@ -0,0 +1 @@
+loci.formats.filter.LZ4Filter$LZ4FilterProvider

components/formats-gpl/src/loci/formats/filter/LZ4Filter.java

@@ -0,0 +1,98 @@
+/*
+ * #%L
+ * OME Bio-Formats package for reading and converting biological file formats.
+ * %%
+ * Copyright (C) 2005 - 2017 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 2 of the 
+ * License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public 
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/gpl-2.0.html>.
+ * #L%
+ */
+
+package loci.formats.filter;
+
+import ucar.nc2.filter.FilterProvider;
+import ucar.nc2.filter.Filter;
+
+import io.airlift.compress.lz4.Lz4Decompressor;
+
+import java.util.Map;
+import java.io.IOException;
+import java.nio.ByteBuffer;
+
+public class LZ4Filter extends Filter {
+
+  static final String name = "LZ4 filter";
+  static final int id = 32004;
+  private Lz4Decompressor decompressor;
+
+  public LZ4Filter(Map<String, Object> properties) {
+    decompressor = new Lz4Decompressor();
+  }
+
+  @Override
+  public String getName() {
+    return name;
+  }
+
+  @Override
+  public int getId() {
+    return id;
+  }
+
+  @Override
+  public byte[] encode(byte[] dataIn) throws IOException {
+    throw new UnsupportedOperationException("LZ4Filter does not support data compression");
+  }
+
+  @Override
+  public byte[] decode(byte[] dataIn) throws IOException {
+    ByteBuffer byteBuffer = ByteBuffer.wrap(dataIn);
+
+    long totalDecompressedSize = byteBuffer.getLong();
+    int decompressedBlockSize = byteBuffer.getInt();
+    int compressedBlockSize = byteBuffer.getInt();
+
+    byte[] decompressedBlock = new byte[Math.toIntExact(totalDecompressedSize)];
+    byte[] compressedBlock = new byte[compressedBlockSize];
+
+    byteBuffer.get(compressedBlock, 0, compressedBlockSize);
+    decompressor.decompress(compressedBlock, 0, compressedBlockSize, decompressedBlock, 0, decompressedBlockSize);
+
+    return decompressedBlock;
+  }
+
+  public static class LZ4FilterProvider implements FilterProvider {
+
+    @Override
+    public String getName() {
+      return name;
+    }
+
+    @Override
+    public int getId() {
+      return id;
+    }
+
+    @Override
+    public Filter create(Map<String, Object> properties) {
+      return new LZ4Filter(properties);
+    }
+
+  }
+
+}

components/formats-gpl/src/loci/formats/in/ImarisHDFReader.java

@@ -28,6 +28,7 @@
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Hashtable;
 
 import loci.common.DataTools;
 import loci.common.Location;
@@ -71,6 +72,15 @@ public class ImarisHDFReader extends SubResolutionFormatReader {
   private List<double[]> colors;
   private int lastChannel = 0;
 
+  // caching parameters
+  private long maxBufferSize = 1024 * 1024 * 1024;
+  private Object[] buffer = null;
+  private int[] blockSizeZPerResolution;
+  private int lastMinZ = 0;
+  private int lastMaxZ = 0;
+  private int lastRes = 0;
+  private int lastT = 0;
+
   // -- Constructor --
 
   /** Constructs a new Imaris HDF reader. */
@@ -223,6 +233,10 @@ public void close(boolean fileOnly) throws IOException {
       pixelSizeX = pixelSizeY = pixelSizeZ = 0;
       minX = minY = minZ = maxX = maxY = maxZ = 0;
 
+      lastRes = lastT = lastMinZ = lastMaxZ = 0;
+      buffer = null;
+      blockSizeZPerResolution = null;
+
       if (netcdf != null) netcdf.close();
       netcdf = null;
 
@@ -300,12 +314,22 @@ protected void initFile(String id) throws FormatException, IOException {
     ms0.thumbnail = false;
     ms0.dimensionOrder = "XYZCT";
 
+    // read block sizes for caching
+    blockSizeZPerResolution = new int[seriesCount];
+    for (int res = 0; res < seriesCount; res++) {
+      String datasetPath = "DataSet/ResolutionLevel_" + res + "/TimePoint_0/Channel_0/Data";
+      Hashtable<String, Object> table = netcdf.getVariableAttributes(datasetPath);
+      String chunkSizesString = (String) table.get("_ChunkSizes");
+      String[] sizes = chunkSizesString.split(" ");
+      blockSizeZPerResolution[res] = Integer.parseInt(sizes[0]);
+    }
+
     // determine pixel type - this isn't stored in the metadata, so we need
     // to check the pixels themselves
 
     int type = -1;
 
-    Object pix = getImageData(0, 0, 0, 1, 1);
+    Object pix = getSampleData();
     if (pix instanceof byte[][]) type = FormatTools.UINT8;
     else if (pix instanceof short[][]) type = FormatTools.UINT16;
     else if (pix instanceof int[][]) type = FormatTools.UINT32;
@@ -434,8 +458,7 @@ private Object getImageData(int no, int x, int y, int width, int height)
     throws FormatException
   {
     int[] zct = getZCTCoords(no);
-    String path = "/DataSet/ResolutionLevel_" + getCoreIndex() + "/TimePoint_" +
-      zct[2] + "/Channel_" + zct[1] + "/Data";
+    int resolutionIndex = getCoreIndex();
     Object image = null;
 
     // the width and height cannot be 1, because then netCDF will give us a
@@ -467,14 +490,110 @@ private Object getImageData(int no, int x, int y, int width, int height)
       x = (getSizeX() / 2) - 1;
     }
 
-    int[] dimensions = new int[] {1, height, width};
-    int[] indices = new int[] {zct[0], y, x};
+    // cache dataset blocks to avoid multiple reads.
+    // use caching for 3D datasets and only if the size of the required buffer is < maxBufferSize
+    if (getSizeZ() > 1 && getSizeX() * getSizeY() * blockSizeZPerResolution[resolutionIndex] * getSizeC() * FormatTools.getBytesPerPixel(getPixelType()) < maxBufferSize) {
+      // update buffer if needed
+      if (zct[0] < lastMinZ || zct[0] > lastMaxZ || zct[2] != lastT || resolutionIndex != lastRes || buffer == null) {
+        buffer = new Object[getSizeC()];
+        if (resolutionIndex != lastRes) {
+          lastRes = resolutionIndex;
+          lastT = zct[2];
+        }
+        if (zct[2] != lastT) {
+          lastT = zct[2];
+        }
+
+        int blockNumber = zct[0] / blockSizeZPerResolution[resolutionIndex];
+        int[] dims = new int[] {blockSizeZPerResolution[resolutionIndex], getSizeY(), getSizeX()};
+        int[] idcs = new int[] {blockNumber * blockSizeZPerResolution[resolutionIndex], 0, 0};
+        try {
+          String path;
+          for (int ch = 0; ch < getSizeC(); ch++) {
+            path = "/DataSet/ResolutionLevel_" + resolutionIndex + "/TimePoint_" + zct[2] + "/Channel_" + ch + "/Data";
+            buffer[ch] = netcdf.getArray(path, idcs, dims);
+          }
+        }
+        catch (ServiceException e) {
+          throw new FormatException(e);
+        }
+
+        lastMinZ = blockNumber * blockSizeZPerResolution[resolutionIndex];
+        lastMaxZ = lastMinZ + blockSizeZPerResolution[resolutionIndex] - 1;
+      }
+
+      // read from buffer
+      if (buffer[zct[1]] instanceof byte[][][]) {
+        byte[][][] byteBuffer = (byte[][][]) buffer[zct[1]];
+        byte[][] slice = new byte[height][width];
+        for (int i = y; i < y + height; i++) {
+          for (int j = x; j < x + width; j++) {
+            slice[i - y][j - x] = byteBuffer[zct[0] - lastMinZ][i][j];
+          }
+        }
+        image = (Object) slice;
+      }
+      else if (buffer[zct[1]] instanceof short[][][]) {
+        short[][][] shortBuffer = (short[][][]) buffer[zct[1]];
+        short[][] slice = new short[height][width];
+        for (int i = y; i < y + height; i++) {
+          for (int j = x; j < x + width; j++) {
+            slice[i - y][j - x] = shortBuffer[zct[0] - lastMinZ][i][j];
+          }
+        }
+        image = (Object) slice;
+      }
+      else if (buffer[zct[1]] instanceof int[][][]) {
+        int[][][] intBuffer = (int[][][]) buffer[zct[1]];
+        int[][] slice = new int[height][width];
+        for (int i = y; i < y + height; i++) {
+          for (int j = x; j < x + width; j++) {
+            slice[i - y][j - x] = intBuffer[zct[0] - lastMinZ][i][j];
+          }
+        }
+        image = (Object) slice;
+      }
+      else if (buffer[zct[1]] instanceof float[][][]) {
+        float[][][] floatBuffer = (float[][][]) buffer[zct[1]];
+        float[][] slice = new float[height][width];
+        for (int i = y; i < y + height; i++) {
+          for (int j = x; j < x + width; j++) {
+            slice[i - y][j - x] = floatBuffer[zct[0] - lastMinZ][i][j];
+          }
+        }
+        image = (Object) slice;
+      }
+    }
+    else {
+      int[] dimensions = new int[] {1, height, width};
+      int[] indices = new int[] {zct[0], y, x};
+      try {
+        String path = "/DataSet/ResolutionLevel_" + resolutionIndex + "/TimePoint_" + zct[2] + "/Channel_" + zct[1] + "/Data";
+        image = netcdf.getArray(path, indices, dimensions);
+      }
+      catch (ServiceException e) {
+        throw new FormatException(e);
+      }
+    }
+
+    return image;
+  }
+
+  private Object getSampleData()
+    throws FormatException
+  {
+    int resolutionIndex = getCoreIndex();
+    Object image = null;
+    int[] dimensions = new int[] {1, 2, 2};
+    int[] indices = new int[] {0, 0, 0};
     try {
+      String path = "/DataSet/ResolutionLevel_" + resolutionIndex + "/TimePoint_0/Channel_0/Data";
       image = netcdf.getArray(path, indices, dimensions);
     }
     catch (ServiceException e) {
       throw new FormatException(e);
     }
+
     return image;
   }
 

components/formats-gpl/src/loci/formats/services/NetCDFServiceImpl.java

@@ -45,6 +45,7 @@
 import ucar.nc2.Attribute;
 import ucar.nc2.Group;
 import ucar.nc2.NetcdfFile;
+import ucar.nc2.NetcdfFiles;
 import ucar.nc2.Variable;
 
 import com.esotericsoftware.kryo.Kryo;
@@ -247,7 +248,7 @@ private void parseAttributesAndVariables(List<Group> groups) {
         if (!groupName.endsWith("/")) variableName = "/" + variableName;
         variableList.add(variableName);
       }
-      groups = group.getGroups();
+      groups = (List<Group>) group.getGroups();
       parseAttributesAndVariables(groups);
     }
   }
@@ -307,7 +308,7 @@ public void print(String s) { }
     };
     System.setOut(throwaway);
     throwaway.close();
-    netCDFFile = NetcdfFile.open(currentId);
+    netCDFFile = NetcdfFiles.open(currentId);
     System.setOut(outStream);
     root = netCDFFile.getRootGroup();
   }