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

…icom-performance
ome · Aug 16, 2024 · ee861f7 · ee861f7
2 parents 4ea1fce + 0a895ae
commit ee861f7
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Showing 114 changed files with 1,645 additions and 1,041 deletions.
diff --git a/.github/workflows/ant.yml b/.github/workflows/ant.yml
@@ -13,7 +13,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up JDK ${{ matrix.java }}
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: ${{ matrix.java }}
           distribution: 'zulu'
@@ -24,7 +24,7 @@ jobs:
       - name: Upload artifacts
         # upload just one set of artifacts for easier PR review
         if: matrix.os == 'ubuntu-latest' && matrix.java == '8'
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           path: artifacts/
           retention-days: 30
diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
@@ -15,13 +15,16 @@ jobs:
       matrix:
         java: [8, 11, 17]
         os: [ubuntu-latest, windows-latest, macos-latest]
+        include:
+          - java: '21'
+            os: 'macos-14'
     runs-on: ${{ matrix.os }}
     env:
       maven_commands: install # default is install
     steps:
       - uses: actions/checkout@v4
       - name: Set up JDK ${{ matrix.java }}
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: ${{ matrix.java }}
           distribution: 'zulu'
@@ -33,7 +36,7 @@ jobs:
     needs: build
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Retrieve version
         id: get_version
         run: |
@@ -48,7 +51,7 @@ jobs:
               echo server='ome.releases' >> $GITHUB_OUTPUT
           fi
       - name: Set up Repository
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 8
           distribution: 'zulu'
@@ -66,7 +69,7 @@ jobs:
     needs: build
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Retrieve version
         id: get_version
         run: |
@@ -81,7 +84,7 @@ jobs:
             echo server='ome.releases' >> $GITHUB_OUTPUT
           fi
       - name: Set up Repository
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 8
           distribution: 'zulu'

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -11,7 +11,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
       - name: Set up JDK
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 8
           distribution: 'zulu'

diff --git a/components/bio-formats-plugins/src/loci/plugins/config/ConfigWindow.java b/components/bio-formats-plugins/src/loci/plugins/config/ConfigWindow.java
@@ -349,7 +349,7 @@ public void run() {
     log.println("-- Formats --");
     try {
       Class<?> irClass = Class.forName("loci.formats.ImageReader");
-      Object ir = irClass.newInstance();
+      Object ir = irClass.getDeclaredConstructor().newInstance();
       Method getClasses = irClass.getMethod("getReaders");
       Object[] readers = (Object[]) getClasses.invoke(ir);
       for (int i=0; i<readers.length; i++) {
@@ -395,7 +395,7 @@ public void run() {
     String matlabVersion = null;
     try {
       Class<?> matlabClass = Class.forName("com.mathworks.jmi.Matlab");
-      Object matlab = matlabClass.newInstance();
+      Object matlab = matlabClass.getDeclaredConstructor().newInstance();
       Method eval = matlabClass.getMethod("eval", new Class[] {String.class});
 
       String ans = (String) eval.invoke(matlab, new Object[] {"version"});

diff --git a/components/bio-formats-plugins/src/loci/plugins/config/FormatEntry.java b/components/bio-formats-plugins/src/loci/plugins/config/FormatEntry.java
@@ -72,7 +72,7 @@ public FormatEntry(PrintWriter log, Object reader) {
     String fwClassName = "loci.plugins.config." + readerName + "Widgets";
     try {
       Class<?> fwClass = Class.forName(fwClassName);
-      fw = (IFormatWidgets) fwClass.newInstance();
+      fw = (IFormatWidgets) fwClass.getDeclaredConstructor().newInstance();
       log.println("Initialized extra widgets for " + readerName + " reader.");
     }
     catch (Throwable t) {

diff --git a/components/bio-formats-plugins/src/loci/plugins/in/IdDialog.java b/components/bio-formats-plugins/src/loci/plugins/in/IdDialog.java
@@ -167,7 +167,7 @@ else if (options.isOMERO()) {
       String group = gd.getNextString();
       Long groupID = null;
       try {
-        groupID = new Long(group);
+        groupID = Long.parseLong(group);
       }
       catch (NumberFormatException e) { }
 

diff --git a/components/bio-formats-plugins/src/loci/plugins/in/ImporterMetadata.java b/components/bio-formats-plugins/src/loci/plugins/in/ImporterMetadata.java
@@ -82,18 +82,18 @@ public ImporterMetadata(IFormatReader r, ImportProcess process,
 
       // merge core values
       final String pad = " "; // puts core values first when alphabetizing
-      put(pad + s + "SizeX", new Integer(r.getSizeX()));
-      put(pad + s + "SizeY", new Integer(r.getSizeY()));
-      put(pad + s + "SizeZ", new Integer(r.getSizeZ()));
-      put(pad + s + "SizeT", new Integer(r.getSizeT()));
-      put(pad + s + "SizeC", new Integer(r.getSizeC()));
-      put(pad + s + "IsRGB", new Boolean(r.isRGB()));
+      put(pad + s + "SizeX", Integer.valueOf(r.getSizeX()));
+      put(pad + s + "SizeY", Integer.valueOf(r.getSizeY()));
+      put(pad + s + "SizeZ", Integer.valueOf(r.getSizeZ()));
+      put(pad + s + "SizeT", Integer.valueOf(r.getSizeT()));
+      put(pad + s + "SizeC", Integer.valueOf(r.getSizeC()));
+      put(pad + s + "IsRGB", Boolean.valueOf(r.isRGB()));
       put(pad + s + "PixelType",
         FormatTools.getPixelTypeString(r.getPixelType()));
-      put(pad + s + "LittleEndian", new Boolean(r.isLittleEndian()));
+      put(pad + s + "LittleEndian", Boolean.valueOf(r.isLittleEndian()));
       put(pad + s + "DimensionOrder", r.getDimensionOrder());
-      put(pad + s + "IsInterleaved", new Boolean(r.isInterleaved()));
-      put(pad + s + "BitsPerPixel", new Integer(r.getBitsPerPixel()));
+      put(pad + s + "IsInterleaved", Boolean.valueOf(r.isInterleaved()));
+      put(pad + s + "BitsPerPixel", Integer.valueOf(r.getBitsPerPixel()));
 
       String seriesName = process.getOMEMetadata().getImageName(i);
       put(pad + "Series " + i + " Name", seriesName);

diff --git a/components/bio-formats-plugins/src/loci/plugins/macro/LociFunctions.java b/components/bio-formats-plugins/src/loci/plugins/macro/LociFunctions.java
@@ -127,25 +127,25 @@ public void getVersionNumber(String[] version) {
   // -- LociFunctions API methods - loci.formats.IFormatReader --
 
   public void getImageCount(Double[] imageCount) {
-    imageCount[0] = new Double(r.getImageCount());
+    imageCount[0] = Double.valueOf(r.getImageCount());
   }
 
-  public void getSizeX(Double[] sizeX) { sizeX[0] = new Double(r.getSizeX()); }
-  public void getSizeY(Double[] sizeY) { sizeY[0] = new Double(r.getSizeY()); }
-  public void getSizeZ(Double[] sizeZ) { sizeZ[0] = new Double(r.getSizeZ()); }
-  public void getSizeC(Double[] sizeC) { sizeC[0] = new Double(r.getSizeC()); }
-  public void getSizeT(Double[] sizeT) { sizeT[0] = new Double(r.getSizeT()); }
+  public void getSizeX(Double[] sizeX) { sizeX[0] = Double.valueOf(r.getSizeX()); }
+  public void getSizeY(Double[] sizeY) { sizeY[0] = Double.valueOf(r.getSizeY()); }
+  public void getSizeZ(Double[] sizeZ) { sizeZ[0] = Double.valueOf(r.getSizeZ()); }
+  public void getSizeC(Double[] sizeC) { sizeC[0] = Double.valueOf(r.getSizeC()); }
+  public void getSizeT(Double[] sizeT) { sizeT[0] = Double.valueOf(r.getSizeT()); }
 
   public void getPixelType(String[] pixelType) {
     pixelType[0] = FormatTools.getPixelTypeString(r.getPixelType());
   }
 
   public void getEffectiveSizeC(Double[] effectiveSizeC) {
-    effectiveSizeC[0] = new Double(r.getEffectiveSizeC());
+    effectiveSizeC[0] = Double.valueOf(r.getEffectiveSizeC());
   }
 
   public void getRGBChannelCount(Double[] rgbChannelCount) {
-    rgbChannelCount[0] = new Double(r.getRGBChannelCount());
+    rgbChannelCount[0] = Double.valueOf(r.getRGBChannelCount());
   }
 
   public void isIndexed(String[] indexed) {
@@ -154,33 +154,33 @@ public void isIndexed(String[] indexed) {
 
   public void getChannelDimCount(Double[] channelDimCount) {
     Modulo moduloC = r.getModuloC();
-    channelDimCount[0] = new Double(moduloC.length() > 1 ? 2 : 1);
+    channelDimCount[0] = Double.valueOf(moduloC.length() > 1 ? 2 : 1);
   }
 
   public void getChannelDimLength(Double i, Double[] channelDimLength) {
     Modulo moduloC = r.getModuloC();
     if (i.intValue() == 0) { // index 0
-      channelDimLength[0] = new Double(moduloC.length() > 1 ? r.getSizeC() / moduloC.length() : r.getSizeC());
+      channelDimLength[0] = Double.valueOf(moduloC.length() > 1 ? r.getSizeC() / moduloC.length() : r.getSizeC());
     } else { // index 1
-      channelDimLength[0] = new Double(moduloC.length());
+      channelDimLength[0] = Double.valueOf(moduloC.length());
     }
   }
 
   public void getChannelDimType(Double i, Double[] channelDimType) {
     Modulo moduloC = r.getModuloC();
     if (i.intValue() == 0) { // index 0
-      channelDimType[0] = new Double(moduloC.length() > 1 ? moduloC.parentType : FormatTools.CHANNEL);
+      channelDimType[0] = Double.valueOf(moduloC.length() > 1 ? moduloC.parentType : FormatTools.CHANNEL);
     } else { // index 1
-      channelDimType[0] = new Double(moduloC.type);
+      channelDimType[0] = Double.valueOf(moduloC.type);
     }
   }
 
 //  public void getThumbSizeX(Double[] thumbSizeX) {
-//    thumbSizeX[0] = new Double(r.getThumbSizeX());
+//    thumbSizeX[0] = Double.valueOf(r.getThumbSizeX());
 //  }
 
 //  public void getThumbSizeY(Double[] thumbSizeY) {
-//    thumbSizeY[0] = new Double(r.getThumbSizeY());
+//    thumbSizeY[0] = Double.valueOf(r.getThumbSizeY());
 //  }
 
   public void isLittleEndian(String[] littleEndian) {
@@ -270,7 +270,7 @@ public void openImage(String title, Double no)
     throws FormatException, IOException
   {
     openSubImage(title, no, 0d, 0d,
-      new Double(r.getSizeX()), new Double(r.getSizeY()));
+      Double.valueOf(r.getSizeX()), Double.valueOf(r.getSizeY()));
   }
 
   public void openSubImage(String title, Double no, Double x, Double y,
@@ -310,7 +310,7 @@ public void openSubImage(String title, Double no, Double x, Double y,
   public void closeFileOnly() throws IOException { r.close(true); }
 
   public void getSeriesCount(Double[] seriesCount) {
-    seriesCount[0] = new Double(r.getSeriesCount());
+    seriesCount[0] = Double.valueOf(r.getSeriesCount());
   }
 
   public void setSeries(Double seriesNum) {
@@ -323,23 +323,23 @@ public void setSeries(Double seriesNum) {
   }
 
   public void getSeries(Double[] seriesNum) {
-    seriesNum[0] = new Double(r.getSeries());
+    seriesNum[0] = Double.valueOf(r.getSeries());
   }
 
   public void setNormalized(Boolean normalize) {
     r.setNormalized(normalize.booleanValue());
   }
 
   public void isNormalized(Boolean[] normalize) {
-    normalize[0] = new Boolean(r.isNormalized());
+    normalize[0] = Boolean.valueOf(r.isNormalized());
   }
 
   public void setOriginalMetadataPopulated(Boolean populate) {
     r.setOriginalMetadataPopulated(populate.booleanValue());
   }
 
   public void isOriginalMetadataPopulated(Boolean[] populate) {
-    populate[0] = new Boolean(r.isOriginalMetadataPopulated());
+    populate[0] = Boolean.valueOf(r.isOriginalMetadataPopulated());
   }
 
   public void setGroupFiles(String groupFiles) {
@@ -373,7 +373,7 @@ public void fileGroupOption(String id, String[] fileGroupOption)
   }
 
   public void getUsedFileCount(Double[] count) {
-    count[0] = new Double(r.getUsedFiles().length);
+    count[0] = Double.valueOf(r.getUsedFiles().length);
   }
 
   public void getUsedFile(Double i, String[] used) {
@@ -385,14 +385,14 @@ public void getCurrentFile(String[] file) {
   }
 
   public void getIndex(Double z, Double c, Double t, Double[] index) {
-    index[0] = new Double(r.getIndex(z.intValue(), c.intValue(), t.intValue()));
+    index[0] = Double.valueOf(r.getIndex(z.intValue(), c.intValue(), t.intValue()));
   }
 
   public void getZCTCoords(Double index, Double[] z, Double[] c, Double[] t) {
     int[] zct = r.getZCTCoords(index.intValue());
-    z[0] = new Double(zct[0]);
-    c[0] = new Double(zct[1]);
-    t[0] = new Double(zct[2]);
+    z[0] = Double.valueOf(zct[0]);
+    c[0] = Double.valueOf(zct[1]);
+    t[0] = Double.valueOf(zct[2]);
   }
 
   public void getMetadataValue(String field, String[] value) {
@@ -472,7 +472,7 @@ public void getPlaneTimingExposureTime(Double[] exposureTime, Double no) {
         val = valTime.value(UNITS.SECOND).doubleValue();
       }
     }
-    exposureTime[0] = val == null ? new Double(Double.NaN) : val;
+    exposureTime[0] = val == null ? Double.NaN : val;
   }
 
   public void getPlanePositionX(Double[] positionX, Double no) {
@@ -524,7 +524,7 @@ public void getPixelsPhysicalSizeX(Double[] sizeX) {
     if (x != null) {
       sizeX[0] = x.value(UNITS.MICROMETER).doubleValue();
     }
-    if (sizeX[0] == null) sizeX[0] = new Double(Double.NaN);
+    if (sizeX[0] == null) sizeX[0] = Double.NaN;
   }
 
   public void getPixelsPhysicalSizeY(Double[] sizeY) {
@@ -534,7 +534,7 @@ public void getPixelsPhysicalSizeY(Double[] sizeY) {
     if (y != null) {
       sizeY[0] = y.value(UNITS.MICROMETER).doubleValue();
     }
-    if (sizeY[0] == null) sizeY[0] = new Double(Double.NaN);
+    if (sizeY[0] == null) sizeY[0] = Double.NaN;
   }
 
   public void getPixelsPhysicalSizeZ(Double[] sizeZ) {
@@ -544,14 +544,14 @@ public void getPixelsPhysicalSizeZ(Double[] sizeZ) {
     if (z != null) {
       sizeZ[0] = z.value(UNITS.MICROMETER).doubleValue();
     }
-    if (sizeZ[0] == null) sizeZ[0] = new Double(Double.NaN);
+    if (sizeZ[0] == null) sizeZ[0] = Double.NaN;
   }
 
   public void getPixelsTimeIncrement(Double[] sizeT) {
     int imageIndex = r.getSeries();
     MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore();
     sizeT[0] = retrieve.getPixelsTimeIncrement(imageIndex).value(UNITS.SECOND).doubleValue();
-    if (sizeT[0] == null) sizeT[0] = new Double(Double.NaN);
+    if (sizeT[0] == null) sizeT[0] = Double.NaN;
   }
 
   // -- PlugIn API methods --

diff --git a/components/bio-formats-plugins/src/loci/plugins/out/Exporter.java b/components/bio-formats-plugins/src/loci/plugins/out/Exporter.java
@@ -517,7 +517,7 @@ else if (FormatTools.isSigned(originalType)) {
             store.setPixelsPhysicalSizeX(FormatTools.getPhysicalSizeX(cal.pixelWidth, cal.getXUnit()), 0);
             store.setPixelsPhysicalSizeY(FormatTools.getPhysicalSizeY(cal.pixelHeight, cal.getYUnit()), 0);
             store.setPixelsPhysicalSizeZ(FormatTools.getPhysicalSizeZ(cal.pixelDepth, cal.getZUnit()), 0);
-            store.setPixelsTimeIncrement(FormatTools.getTime(new Double(cal.frameInterval), cal.getTimeUnit()), 0);
+            store.setPixelsTimeIncrement(FormatTools.getTime(Double.valueOf(cal.frameInterval), cal.getTimeUnit()), 0);
 
             if (imp.getImageStackSize() !=
                     imp.getNChannels() * imp.getNSlices() * imp.getNFrames())

diff --git a/components/bio-formats-plugins/src/loci/plugins/util/ROIHandler.java b/components/bio-formats-plugins/src/loci/plugins/util/ROIHandler.java
@@ -745,10 +745,10 @@ private static void storePoint(PointRoi roi, MetadataStore store,
   private static void storeLine(Line roi, MetadataStore store,
       int roiNum, int shape, int c, int z, int t)
   {
-    store.setLineX1(new Double(roi.x1), roiNum, shape);
-    store.setLineX2(new Double(roi.x2), roiNum, shape);
-    store.setLineY1(new Double(roi.y1), roiNum, shape);
-    store.setLineY2(new Double(roi.y2), roiNum, shape);
+    store.setLineX1(Double.valueOf(roi.x1), roiNum, shape);
+    store.setLineX2(Double.valueOf(roi.x2), roiNum, shape);
+    store.setLineY1(Double.valueOf(roi.y1), roiNum, shape);
+    store.setLineY2(Double.valueOf(roi.y2), roiNum, shape);
     if (c >= 0) {
       store.setLineTheC(unwrap(c), roiNum, shape);
     }
@@ -787,10 +787,10 @@ private static void storeRectangle(Roi roi, MetadataStore store,
       int roiNum, int shape, int c, int z, int t)
   {
     Rectangle bounds = roi.getBounds();
-    store.setRectangleX(new Double(bounds.x), roiNum, shape);
-    store.setRectangleY(new Double(bounds.y), roiNum, shape);
-    store.setRectangleWidth(new Double(bounds.width), roiNum, shape);
-    store.setRectangleHeight(new Double(bounds.height), roiNum, shape);
+    store.setRectangleX(Double.valueOf(bounds.x), roiNum, shape);
+    store.setRectangleY(Double.valueOf(bounds.y), roiNum, shape);
+    store.setRectangleWidth(Double.valueOf(bounds.width), roiNum, shape);
+    store.setRectangleHeight(Double.valueOf(bounds.height), roiNum, shape);
     if (c >= 0) {
       store.setRectangleTheC(unwrap(c), roiNum, shape);
     }