Merge branch 'develop' into release_artifacts

.github/workflows/ant.yml

@@ -7,7 +7,7 @@ jobs:
   build:
     strategy:
       matrix:
-        java: [1.8, 11]
+        java: [1.8, 11, 17]
         os: [ubuntu-latest, windows-latest]
     runs-on: ${{ matrix.os }}
     steps:
@@ -20,3 +20,10 @@ jobs:
         run: |
             ./tools/test-build ant
             ant docs
+      - name: Upload artifacts
+        # upload just one set of artifacts for easier PR review
+        if: matrix.os == 'ubuntu-latest' && matrix.java == '1.8'
+        uses: actions/upload-artifact@v3
+        with:
+          path: artifacts/
+          retention-days: 30

.github/workflows/maven.yml

@@ -13,7 +13,7 @@ jobs:
   build:
     strategy:
       matrix:
-        java: [1.8, 11]
+        java: [1.8, 11, 17]
         os: [ubuntu-latest, windows-latest, macos-latest]
     runs-on: ${{ matrix.os }}
     env:

components/bio-formats-plugins/pom.xml

@@ -72,11 +72,13 @@
       <groupId>ch.qos.logback</groupId>
       <artifactId>logback-core</artifactId>
       <version>${logback.version}</version>
+      <optional>true</optional>
     </dependency>
     <dependency>
       <groupId>ch.qos.logback</groupId>
       <artifactId>logback-classic</artifactId>
       <version>${logback.version}</version>
+      <optional>true</optional>
     </dependency>
 
     <!-- NB: dependency:analyze has false warning about xml-apis:xml-apis. -->

components/bio-formats-tools/pom.xml

@@ -67,13 +67,15 @@
       <artifactId>logback-core</artifactId>
       <version>${logback.version}</version>
       <scope>runtime</scope>
+      <optional>true</optional>
     </dependency>
     <dependency>
       <!-- NB: We want this, despite warning from dependency:analyze. -->
       <groupId>ch.qos.logback</groupId>
       <artifactId>logback-classic</artifactId>
       <version>${logback.version}</version>
       <scope>runtime</scope>
+      <optional>true</optional>
     </dependency>
     <dependency>
       <!-- NB: We want this, despite warning from dependency:analyze. -->

components/formats-bsd/src/loci/formats/in/JPEGReader.java

@@ -180,7 +180,7 @@ public void close(boolean fileOnly) throws IOException {
 
   // -- Helper reader --
 
-  static class DefaultJPEGReader extends ImageIOReader {
+  public static class DefaultJPEGReader extends ImageIOReader {
     public DefaultJPEGReader() {
       super("JPEG", new String[] {"jpg", "jpeg", "jpe"});
       suffixNecessary = false;

components/formats-gpl/src/loci/formats/in/CV7000Reader.java

@@ -79,7 +79,6 @@ public class CV7000Reader extends FormatReader {
   // -- Fields --
 
   private String[] allFiles;
-  private Location parent;
   private MinimalTiffReader reader;
   private String wppPath;
   private String detailPath;
@@ -239,7 +238,7 @@ protected void initFile(String id) throws FormatException, IOException {
     String wpiXML = readSanitizedXML(id);
     XMLTools.parseXML(wpiXML, plate);
 
-    parent = new Location(id).getAbsoluteFile().getParentFile();
+    Location parent = new Location(id).getAbsoluteFile().getParentFile();
     allFiles = parent.list(true);
     Arrays.sort(allFiles);
     for (int i=0; i<allFiles.length; i++) {

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

@@ -376,6 +376,8 @@ public class CellSensReader extends FormatReader {
   // -- Fields --
 
   private String[] usedFiles;
+  // non-pixels files that are included in the directory (e.g. "blobs")
+  private ArrayList<String> extraFiles = new ArrayList<String>();
   private HashMap<Integer, String> fileMap = new HashMap<Integer, String>();
 
   private TiffParser parser;
@@ -451,7 +453,15 @@ public String[] getSeriesUsedFiles(boolean noPixels) {
     FormatTools.assertId(currentId, true, 1);
 
     // all files contain pixels
-    return noPixels ? null : usedFiles;
+    if (noPixels) {
+      return extraFiles.toArray(new String[extraFiles.size()]);
+    }
+    String[] allFiles = new String[extraFiles.size() + usedFiles.length];
+    System.arraycopy(usedFiles, 0, allFiles, 0, usedFiles.length);
+    for (int i=0; i<extraFiles.size(); i++) {
+      allFiles[usedFiles.length + i] = extraFiles.get(i);
+    }
+    return allFiles;
   }
 
   /* @see loci.formats.IFormatReader#getOptimalTileWidth() */
@@ -591,6 +601,7 @@ public void close(boolean fileOnly) throws IOException {
       parser = null;
       ifds = null;
       usedFiles = null;
+      extraFiles.clear();
       fileMap.clear();
       tileOffsets.clear();
       jpeg = false;
@@ -673,9 +684,12 @@ protected void initFile(String id) throws FormatException, IOException {
         if (pixelsFiles != null) {
           Arrays.sort(pixelsFiles);
           for (String pixelsFile : pixelsFiles) {
-            if (checkSuffix(pixelsFile, "ets")) {
+            if (checkSuffix(pixelsFile, "ets") && pixelsFile.startsWith("frame_")) {
               files.add(new Location(stackDir, pixelsFile).getAbsolutePath());
             }
+            else {
+              extraFiles.add(new Location(stackDir, pixelsFile).getAbsolutePath());
+            }
           }
         }
       }

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

@@ -111,18 +111,17 @@ public class CellVoyagerReader extends FormatReader
 
   private static final String SINGLE_TIFF_PATH_BUILDER = "W%dF%03dT%04dZ%02dC%d.tif";
 
-  private Location measurementFolder;
-  private Location imageFolder;
+  private String imageFolder;
 
   private List< ChannelInfo > channelInfos;
 
   private List< WellInfo > wells;
 
   private List< Integer > timePoints;
 
-  private Location measurementResultFile;
+  private String measurementResultFile;
 
-  private Location omeMeasurementFile;
+  private String omeMeasurementFile;
 
   public CellVoyagerReader()
   {
@@ -148,8 +147,6 @@ public byte[] openBytes( final int no, final byte[] buf, final int x, final int
     final AreaInfo area = well.areas.get( areaIndex );
     final MinimalTiffReader tiffReader = new MinimalTiffReader();
 
-    imageFolder = new Location(currentId).getAbsoluteFile().getParentFile();
-    imageFolder = new Location(imageFolder, "Image");
     for ( final FieldInfo field : area.fields )
     {
 
@@ -274,7 +271,7 @@ protected void initFile( final String id ) throws FormatException, IOException
   {
     super.initFile( id );
 
-    measurementFolder = new Location( id ).getAbsoluteFile();
+    Location measurementFolder = new Location( id ).getAbsoluteFile();
     if ( !measurementFolder.exists() ) { throw new IOException( "File " + id + " does not exist." ); }
     if ( !measurementFolder.isDirectory() )
     {
@@ -283,22 +280,26 @@ protected void initFile( final String id ) throws FormatException, IOException
         measurementFolder = measurementFolder.getParentFile();
       }
     }
-    imageFolder = new Location(measurementFolder, "Image");
+    imageFolder = new Location(measurementFolder, "Image").getAbsolutePath();
 
-    measurementResultFile = new Location( measurementFolder, "MeasurementResult.xml" );
-    if ( !measurementResultFile.exists() ) { throw new IOException( "Could not find " + measurementResultFile + " in folder." ); }
+    Location measurementResult = new Location( measurementFolder, "MeasurementResult.xml" );
+    if ( !measurementResult.exists() ) { throw new IOException( "Could not find " + measurementResult + " in folder." ); }
+    else {
+      measurementResultFile = measurementResult.getAbsolutePath();
+    }
 
-    omeMeasurementFile = new Location( measurementFolder, "MeasurementResult.ome.xml" );
-    if ( !omeMeasurementFile.exists() ) { throw new IOException( "Could not find " + omeMeasurementFile + " in folder." ); }
+    Location omeMeasurement = new Location( measurementFolder, "MeasurementResult.ome.xml" );
+    if ( !omeMeasurement.exists() ) { throw new IOException( "Could not find " + omeMeasurement + " in folder." ); }
+    else {
+      omeMeasurementFile = omeMeasurement.getAbsolutePath();
+    }
 
     /*
      * Open MeasurementSettings file
      */
 
-    RandomAccessInputStream result =
-      new RandomAccessInputStream(measurementResultFile.getAbsolutePath());
     Document msDocument = null;
-    try {
+    try (RandomAccessInputStream result = new RandomAccessInputStream(measurementResultFile)) {
       msDocument = XMLTools.parseDOM(result);
     }
     catch (ParserConfigurationException e) {
@@ -307,9 +308,6 @@ protected void initFile( final String id ) throws FormatException, IOException
     catch (SAXException e) {
       throw new IOException(e);
     }
-    finally {
-      result.close();
-    }
 
     msDocument.getDocumentElement().normalize();
 
@@ -329,10 +327,9 @@ protected void initFile( final String id ) throws FormatException, IOException
      * Open OME metadata file
      */
 
-    RandomAccessInputStream measurement =
-      new RandomAccessInputStream(omeMeasurementFile.getAbsolutePath());
+
     Document omeDocument = null;
-    try {
+    try (RandomAccessInputStream measurement = new RandomAccessInputStream(omeMeasurementFile)) {
       omeDocument = XMLTools.parseDOM(measurement);
     }
     catch (ParserConfigurationException e) {
@@ -341,9 +338,6 @@ protected void initFile( final String id ) throws FormatException, IOException
     catch (SAXException e) {
       throw new IOException(e);
     }
-    finally {
-      measurement.close();
-    }
     omeDocument.getDocumentElement().normalize();
 
     /*
@@ -361,7 +355,7 @@ public String[] getSeriesUsedFiles( final boolean noPixels )
 
     if ( noPixels )
     {
-      return new String[] { measurementResultFile.getAbsolutePath(), omeMeasurementFile.getAbsolutePath() };
+      return new String[] { measurementResultFile, omeMeasurementFile };
     }
     else
     {
@@ -371,8 +365,8 @@ public String[] getSeriesUsedFiles( final boolean noPixels )
       final AreaInfo area = wells.get( wellIndex ).areas.get( areaIndex );
       final int nFields = area.fields.size();
       ArrayList<String> images = new ArrayList<String>();
-      images.add(measurementResultFile.getAbsolutePath());
-      images.add(omeMeasurementFile.getAbsolutePath());
+      images.add(measurementResultFile);
+      images.add(omeMeasurementFile);
 
       for ( final Integer timepoint : timePoints )
       {

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

@@ -77,6 +77,7 @@ public class LiFlimReader extends FormatReader {
 
   // relevant keys in layout and background tables
   public static final String DATATYPE_KEY = "datatype";
+  public static final String PACKING_KEY = "packing";
   public static final String C_KEY = "channels";
   public static final String X_KEY = "x";
   public static final String Y_KEY = "y";
@@ -120,6 +121,7 @@ public class LiFlimReader extends FormatReader {
   private String version;
   private String compression;
   private String datatype;
+  private String packing;
   private String channels;
   private String xLen;
   private String yLen;
@@ -215,12 +217,14 @@ else if (TypeUINT12) {
           UINT12stream.readFully(bytes);
         }
         catch (EOFException e) {
-          LOGGER.debug("Could not read full 12-bitt plane", e);
+          LOGGER.debug("Could not read full 12-bit plane", e);
         }
 
-        //Covert 12bit data to 16bit data, maintaining 12bit depth.
+        // Covert 12bit data to 16bit data, maintaining 12bit depth.
+        // with msb packing convert in the order of most significant bit, otherwise use least significant bit
         byte[] returnArray = new byte[0];
-        returnArray = convert12to16(bytes); 
+        returnArray = packing.equals("msb") ? 
+          convert12to16MSB(bytes) : convert12to16LSB(bytes);
         RandomAccessInputStream s = new RandomAccessInputStream(returnArray);
         readPlane(s, x, y, w, h, buf);
         s.close();
@@ -255,6 +259,11 @@ public void close(boolean fileOnly) throws IOException {
       version = null;
       compression = null;
       datatype = null;
+      packing = null;
+      if (UINT12stream != null) UINT12stream.close();
+      UINT12stream = null;
+      UINT12streamPos = 0;
+      UINT12streamSeries = 0;
       channels = null;
       xLen = null;
       yLen = null;
@@ -310,6 +319,7 @@ private void initOriginalMetadata() {
 
     IniTable layoutTable = ini.getTable(LAYOUT_TABLE);
     datatype = layoutTable.get(DATATYPE_KEY);
+    packing = layoutTable.get(PACKING_KEY);
     channels = layoutTable.get(C_KEY);
     xLen = layoutTable.get(X_KEY);
     yLen = layoutTable.get(Y_KEY);
@@ -572,10 +582,10 @@ private int getPixelTypeFromString(String type) throws FormatException {
     else if (DATATYPE_REAL64.equals(type)) return FormatTools.DOUBLE;
     /* Check for UINT12, set DataType to UINT16 because core does not support UINT12 */
     else if (DATATYPE_UINT12.equals(type)) 
-    	{ 
+    { 
     	TypeUINT12 = true;
     	return FormatTools.UINT16;
-    	}
+    }
     throw new FormatException("Unknown data type: " + type);
   }
 
@@ -667,25 +677,39 @@ else if (UINT12streamSeries == 1 && DarkImage != null && DarkImage.equals(new St
 
 	  }
 
-  // Added a Function to unpack 12bit data to 16bit data maintaining 12bits depth.
-  private static byte[] convert12to16(byte[] image) {
-	   	byte[] image16 = new byte[image.length * 4 / 3];
-
-
-		if (image16.length / 4 != image.length / 3)
-	  		return new byte[0];
-
-		for (int idx = 0, idx16 = 0; idx < (image.length - 2) && (idx16 < image16.length - 3); idx += 3, idx16 += 4) 
-		{
-	  		image16[idx16] = (byte)(image[idx] & 0xff);
-	  		image16[idx16 + 1] = (byte)((image[idx + 1] & 0x0f));
-	  		image16[idx16 + 2] = (byte)(((image[idx + 1] & 0xf0) >> 4) + ((image[idx + 2] & 0x0f) << 4));
-	  		image16[idx16 + 3] = (byte)((image[idx + 2] & 0xf0) >> 4);
-		}
-
-		return image16;
-		}
+  // Unpack 12bit data by least significant bit first to 16bit data maintaining 12bits depth.
+  private static byte[] convert12to16LSB(byte[] image) {
+    byte[] image16 = new byte[image.length * 4 / 3];
+
+    if (image16.length / 4 != image.length / 3)
+      return new byte[0];
+
+    for (int idx = 0, idx16 = 0; idx < (image.length - 2) && (idx16 < image16.length - 3); idx += 3, idx16 += 4) {
+      image16[idx16] = (byte)(image[idx] & 0xff);
+      image16[idx16 + 1] = (byte)((image[idx + 1] & 0x0f));
+      image16[idx16 + 2] = (byte)(((image[idx + 1] & 0xf0) >> 4) | ((image[idx + 2] & 0x0f) << 4));
+      image16[idx16 + 3] = (byte)((image[idx + 2] & 0xf0) >> 4);
+    }
+
+    return image16;
+  }
+
+  // Unpack 12bit data by most significant bit first to 16bit data maintaining 12bits depth.
+  private static byte[] convert12to16MSB(byte[] image) {
+    byte[] image16 = new byte[image.length * 4 / 3];
+
+    if (image16.length / 4 != image.length / 3)
+      return new byte[0];
+
+    for (int idx = 0, idx16 = 0; idx < (image.length - 2) && (idx16 < image16.length - 3); idx += 3, idx16 += 4) {
+      image16[idx16] = (byte)(((image[idx]  & 0x0f) << 4) | ((image[idx + 1]  & 0xf0) >> 4));
+      image16[idx16 + 1] = (byte)((image[idx]  & 0xf0) >> 4);
+      image16[idx16 + 2] = (byte)((image[idx + 2] & 0xff));
+      image16[idx16 + 3] = (byte)((image[idx + 1]) & 0x0f);
+    }
 
+    return image16;
+  }
 
   private void skip(InputStream is, long num) throws IOException {
     long skipLeft = num;