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

…isable-chroma-subsampling

.classpath-template

@@ -6,8 +6,6 @@
         <classpathentry kind="src" path="components/formats-bsd/src"/>
         <classpathentry kind="src" path="components/formats-gpl/build/src"/>
         <classpathentry kind="src" path="components/formats-gpl/src"/>
-        <classpathentry kind="src" path="components/stubs/lwf-stubs/build/src"/>
-        <classpathentry kind="src" path="components/stubs/lwf-stubs/src"/>
         <classpathentry kind="src" path="components/test-suite/build/src"/>
         <classpathentry kind="src" path="components/test-suite/src"/>
         <classpathentry kind="src" path="components/formats-api/test"/>

.github/workflows/ant.yml

@@ -11,7 +11,7 @@ jobs:
         os: [ubuntu-latest, windows-latest]
     runs-on: ${{ matrix.os }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up JDK ${{ matrix.java }}
         uses: actions/setup-java@v3
         with:

.github/workflows/maven.yml

@@ -19,7 +19,7 @@ jobs:
     env:
       maven_commands: install # default is install
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up JDK ${{ matrix.java }}
         uses: actions/setup-java@v3
         with:
@@ -33,7 +33,7 @@ jobs:
     needs: build
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Retrieve version
         id: get_version
         run: |
@@ -66,7 +66,7 @@ jobs:
     needs: build
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Retrieve version
         id: get_version
         run: |

.github/workflows/release.yml

@@ -9,7 +9,7 @@ jobs:
     name: Release artifacts
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:

build.xml

@@ -16,8 +16,7 @@ Bio-Formats
     JAR file:      bio-formats.jar
     Path:          components/bio-formats
     Project deps:  Formats Common, OME-XML Java library, JAI Image I/O Tools,
-                   MDB Tools (Java port), Apache Jakarta POI,
-                   Luratech LuraWave stubs
+                   MDB Tools (Java port), Apache Jakarta POI
     Library deps:  JGoodies Forms, Logback, NetCDF,
                    Simple Logging Facade for Java API, TestNG
     Optional:      Xalan Serializer, Xalan
@@ -76,21 +75,6 @@ JAI Image I/O Tools
                    This component will be removed once our changes have been
                    added to the official JAI CVS repository.
 
-===============================================================================
-The following components are stubs of third party projects:
-
-Luratech LuraWave stubs
-    Stub of proprietary Java API to handle Luratech LWF compression
-    -=-
-    JAR file:      lwf-stubs.jar
-    Path:          components/stubs/lwf-stubs
-    Project deps:  (none)
-    Optional:      (none)
-    License:       BSD
-    Project URL:   http://www.luratech.com/
-    Notes:         required to compile Bio-Formats's support for Luratech LWF
-                   compression for the Opera Flex format
-
 ===============================================================================
 The following external dependencies (in the jar folder) may be required:
 Ant-Contrib

components/bio-formats-plugins/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>7.0.0-SNAPSHOT</version>
+    <version>7.1.0-SNAPSHOT</version>
     <relativePath>../..</relativePath>
   </parent>
 

components/bio-formats-plugins/src/loci/plugins/config/ConfigWindow.java

@@ -218,7 +218,6 @@ public ConfigWindow() {
     //   + upgrade button for "ImageJ" just launches ImageJ upgrade plugin
     // - can install native libs by downloading installer from its web site
     //   + QuickTime for Java
-    //   + Nikon ND2 plugin
     //   + ImageIO Tools
 
     libInfo.add(makeLabel("Path", false));
@@ -375,18 +374,6 @@ public void run() {
     // Ant replaces date token with datestamp of the build
     if (bfVersion.equals("@" + "date" + "@")) bfVersion = "Internal build";
 
-    String qtVersion = null;
-    try {
-      Class<?> qtToolsClass = Class.forName("loci.formats.gui.LegacyQTTools");
-      Object qtTools = qtToolsClass.newInstance();
-      Method getQTVersion = qtToolsClass.getMethod("getQTVersion");
-      qtVersion = (String) getQTVersion.invoke(qtTools);
-    }
-    catch (Throwable t) {
-      log.println("Could not determine QuickTime version:");
-      t.printStackTrace(log);
-    }
-
     String clibIIOVersion = null;
     try {
       Class<?> jpegSpi = Class.forName(
@@ -428,7 +415,6 @@ public void run() {
     HashMap<String, String> versions = new HashMap<String, String>();
     versions.put("javaVersion", javaVersion);
     versions.put("bfVersion", bfVersion);
-    if (qtVersion != null) versions.put("qtVersion", qtVersion);
     if (clibIIOVersion != null) versions.put("clibIIOVersion", clibIIOVersion);
     if (matlabVersion != null) versions.put("matlabVersion", matlabVersion);
 

components/bio-formats-plugins/src/loci/plugins/config/InstallWizard.java

@@ -83,15 +83,6 @@ public InstallWizard() {
 
     // check for conflicting JARs -- i.e., duplicate classes
 
-    // Win32: download and install QuickTime
-    // Download http://www.apple.com/quicktime/download/
-    // Find line with qtimewin, extract URL
-    // Download the URL
-    // Find line with QuickTimeInstaller.exe, extract URL
-    // Download the URL
-    // Execute program
-    // Wait for process completion before continuing
-
     // Linux: download and install Image I/O Tools native codecs
     // Download http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-lib-linux-i586-jre.bin
     // Chmod 755 and execute?
@@ -105,12 +96,6 @@ public InstallWizard() {
     // Find jre/bin folder by checking ImageJ.cfg file?
     // test with data/dicom/john/E724_S007_A0024.dcm
 
-    // Win32: download and install Nikon ND2 plugin
-    // (gray out option to use Nikon ND2 if plugin is not available)
-    // Download http://rsb.info.nih.gov/ij/plugins/download/jars/ImageJND2ReaderPlugin.zip
-    // Extract .msi file and execute it
-    // Wait for process completion before continuing
-
     // Option to download Image5D
     // Download http://rsb.info.nih.gov/ij/plugins/download/jars/Image_5D.jar
     // Place in ImageJ plugins folder

components/bio-formats-plugins/src/loci/plugins/config/ND2Widgets.java

@@ -35,7 +35,7 @@
 
 import javax.swing.JCheckBox;
 
-import loci.formats.in.NativeND2Reader;
+import loci.formats.in.ND2Reader;
 import loci.plugins.util.LociPrefs;
 
 /**
@@ -53,23 +53,17 @@ public class ND2Widgets implements IFormatWidgets, ItemListener {
   // -- Constructor --
 
   public ND2Widgets() {
-    boolean nikon = Prefs.get(LociPrefs.PREF_ND2_NIKON, false);
-
-    String legacyLabel = "Nikon";
-    JCheckBox legacyBox = new JCheckBox(
-      "Use Nikon's ND2 library instead of native ND2 support", nikon);
-    legacyBox.addItemListener(this);
 
     boolean chunkmap = Prefs.get(LociPrefs.PREF_ND2_CHUNKMAP,
-      NativeND2Reader.USE_CHUNKMAP_DEFAULT);
+      ND2Reader.USE_CHUNKMAP_DEFAULT);
 
     String chunkmapLabel = "Chunkmap";
     JCheckBox chunkmapBox = new JCheckBox(
       "Use chunkmap table to read image offsets", chunkmap);
     chunkmapBox.addItemListener(this);
 
-    labels = new String[] {legacyLabel, chunkmapLabel};
-    widgets = new Component[] {legacyBox, chunkmapBox};
+    labels = new String[] {chunkmapLabel};
+    widgets = new Component[] {chunkmapBox};
   }
 
   // -- IFormatWidgets API methods --
@@ -89,10 +83,7 @@ public Component[] getWidgets() {
   @Override
   public void itemStateChanged(ItemEvent e) {
     JCheckBox box = (JCheckBox) e.getSource();
-    if (box.equals(getWidgets()[0])) {
-      Prefs.set(LociPrefs.PREF_ND2_NIKON, box.isSelected());
-    }
-    else if (box.equals(getWidgets()[1])) {
+    if (box.equals(getWidgets()[1])) {
       Prefs.set(LociPrefs.PREF_ND2_CHUNKMAP, box.isSelected());
     }
   }