Merge branch 'develop' into quick-start-czi-reader

.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:

components/bio-formats-plugins/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>7.0.1-SNAPSHOT</version>
+    <version>7.1.0-SNAPSHOT</version>
     <relativePath>../..</relativePath>
   </parent>
 

components/bio-formats-plugins/src/loci/plugins/out/Exporter.java

@@ -446,6 +446,15 @@ else if (store.getImageCount() > 1) {
             store.setPixelsSizeC(new PositiveInteger(channels*imp.getNChannels()), 0);
             store.setPixelsSizeT(new PositiveInteger(imp.getNFrames()), 0);
 
+            try {
+              // if a subset of the data was opened, the number of Channels
+              // in the OME-XML may not match the ImagePlus channel count
+              // channel count mismatches can cause problems when actually writing pixels
+              service.removeChannels(service.getOMEMetadata(store), 0, imp.getNChannels());
+            }
+            catch (ServiceException e) {
+            }
+
             if (store.getImageID(0) == null) {
                 store.setImageID(MetadataTools.createLSID("Image", 0), 0);
             }

components/bio-formats-tools/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>7.0.1-SNAPSHOT</version>
+    <version>7.1.0-SNAPSHOT</version>
     <relativePath>../..</relativePath>
   </parent>
 

components/bio-formats-tools/src/loci/formats/tools/GenerateCache.java

@@ -9,13 +9,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

components/bundles/bioformats_package/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>7.0.1-SNAPSHOT</version>
+    <version>7.1.0-SNAPSHOT</version>
     <relativePath>../../../</relativePath>
   </parent>
 

components/forks/turbojpeg/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>7.0.1-SNAPSHOT</version>
+    <version>7.1.0-SNAPSHOT</version>
     <relativePath>../../../</relativePath>
   </parent>
 

components/formats-api/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>7.0.1-SNAPSHOT</version>
+    <version>7.1.0-SNAPSHOT</version>
     <relativePath>../..</relativePath>
   </parent>
 

components/formats-api/src/loci/formats/CoreMetadataList.java

@@ -9,13 +9,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

components/formats-api/src/loci/formats/MetadataList.java

@@ -1,6 +1,6 @@
 /*
  * #%L
- * primary reader and writer APIs
+ * Top-level reader and writer APIs
  * %%
  * Copyright (C) 2018 Open Microscopy Environment:
  *   - Board of Regents of the University of Wisconsin-Madison
@@ -9,13 +9,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

components/formats-api/test/loci/formats/utests/CoreMetadataListTest.java

@@ -9,13 +9,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

components/formats-api/test/loci/formats/utests/MetadataListTest.java

@@ -9,13 +9,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

components/formats-bsd/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>7.0.1-SNAPSHOT</version>
+    <version>7.1.0-SNAPSHOT</version>
     <relativePath>../..</relativePath>
   </parent>
 

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

@@ -10,13 +10,13 @@
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
- *
+ * 
  * 1. Redistributions of source code must retain the above copyright notice,
  *    this list of conditions and the following disclaimer.
  * 2. Redistributions in binary form must reproduce the above copyright notice,
  *    this list of conditions and the following disclaimer in the documentation
  *    and/or other materials provided with the distribution.
- *
+ * 
  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE

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

@@ -1103,6 +1103,9 @@ else if (t == 0) {
         if (firstFile == null ||
           (testFile != null && !info[s][0].reader.isThisType(testFile)))
         {
+          if (info[s][0].id != null && failOnMissingTIFF()) {
+            throw new FormatException("Invalid file (may be corrupted): " + info[s][0].id);
+          }
           LOGGER.warn("{} is not a valid OME-TIFF", info[s][0].id);
           info[s][0].id = currentId;
           info[s][0].exists = false;

components/formats-bsd/src/loci/formats/in/SlideBook7Reader.java

@@ -1,26 +1,33 @@
 
 /*
  * #%L
- * OME Bio-Formats package for reading and converting biological file formats.
+ * BSD implementations of Bio-Formats readers and writers
  * %%
  * Copyright (C) 2005 - 2022 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>.
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ * 
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
  * #L%
  */
 

components/formats-bsd/src/loci/formats/out/DicomWriter.java

@@ -188,18 +188,28 @@ public void saveBytes(int no, byte[] buf, int x, int y, int w, int h)
   {
     checkParams(no, buf, x, y, w, h);
 
+    int resolutionIndex = getIndex(series, resolution);
+    int thisTileWidth = tileWidth[resolutionIndex];
+    int thisTileHeight = tileHeight[resolutionIndex];
+
     MetadataRetrieve r = getMetadataRetrieve();
     if ((!(r instanceof IPyramidStore) ||
       ((IPyramidStore) r).getResolutionCount(series) == 1) &&
       !isFullPlane(x, y, w, h))
     {
       throw new FormatException("DicomWriter does not allow tiles for non-pyramid images");
     }
+    else if (x % thisTileWidth != 0 || y % thisTileHeight != 0 ||
+      (w != thisTileWidth && x + w != getSizeX()) ||
+      (h != thisTileHeight && y + h != getSizeY()))
+    {
+      throw new FormatException("Tile too small, expected " + thisTileWidth + "x" + thisTileHeight +
+        ". Setting the tile size to " + getSizeX() + "x" + getSizeY() + " or smaller may work.");
+    }
     checkPixelCount(false);
 
     boolean first = x == 0 && y == 0;
     boolean last = x + w == getSizeX() && y + h == getSizeY();
-    int resolutionIndex = getIndex(series, resolution);
 
     // the compression type isn't supplied to the writer until
     // after setId is called, so metadata that indicates or
@@ -264,8 +274,6 @@ public void saveBytes(int no, byte[] buf, int x, int y, int w, int h)
 
     byte[] paddedBuf = null;
 
-    int thisTileWidth = tileWidth[resolutionIndex];
-    int thisTileHeight = tileHeight[resolutionIndex];
     int thisTilePixels = thisTileWidth * thisTileHeight;
 
     // pad the last row and column of tiles to match specified tile size

components/formats-bsd/src/loci/formats/services/JPEGTurboServiceImpl.java

@@ -105,8 +105,10 @@ public JPEGTurboServiceImpl() {
     logger = Logger.getLogger(NATIVE_LIB_CLASS);
     logger.setLevel(Level.SEVERE);
     if (!libraryLoaded) {
-      NativeLibraryUtil.loadNativeLibrary(TJ.class, "turbojpeg");
-      libraryLoaded = true;
+      libraryLoaded = NativeLibraryUtil.loadNativeLibrary(TJ.class, "turbojpeg");
+      if (!libraryLoaded) {
+        throw new RuntimeException("TurboJPEG could not be loaded");
+      }
     }
   }
 

components/formats-bsd/src/loci/formats/tiff/IFD.java

@@ -615,6 +615,9 @@ public int getPixelType() throws FormatException {
       case 24:
         return FormatTools.FLOAT;
       case 64:
+        if (bitFormat != 3) {
+          throw new FormatException("64-bit int data not supported");
+        }
         return FormatTools.DOUBLE;
       case 32:
         if (bitFormat == 3) return FormatTools.FLOAT;

components/formats-bsd/src/loci/formats/tiff/TiffParser.java

@@ -546,6 +546,9 @@ public Object getIFDValue(TiffIFDEntry entry) throws IOException {
         offset &= 0xffffffffL;
         offset += 0x100000000L;
       }
+      if (offset >= in.length()) {
+        return null;
+      }
       in.seek(offset);
     }
 

components/formats-bsd/test/spec/AbstractTest.java

@@ -1,8 +1,11 @@
 /*
  * #%L
- * Tests for OME-XML specification classes.
+ * BSD implementations of Bio-Formats readers and writers
  * %%
- * Copyright (C) 2010-2013 Glencoe Software, Inc.
+ * Copyright (C) 2005 - 2017 Open Microscopy Environment:
+ *   - Board of Regents of the University of Wisconsin-Madison
+ *   - Glencoe Software, Inc.
+ *   - University of Dundee
  * %%
  * Redistribution and use in source and binary forms, with or without
  * modification, are permitted provided that the following conditions are met:
@@ -24,10 +27,6 @@
  * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
  * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
  * POSSIBILITY OF SUCH DAMAGE.
- * 
- * The views and conclusions contained in the software and documentation are
- * those of the authors and should not be interpreted as representing official
- * policies, either expressed or implied, of any organization.
  * #L%
  */
 

components/formats-gpl/pom.xml

@@ -8,7 +8,7 @@
   <parent>
     <groupId>ome</groupId>
     <artifactId>pom-bio-formats</artifactId>
-    <version>7.0.1-SNAPSHOT</version>
+    <version>7.1.0-SNAPSHOT</version>
     <relativePath>../..</relativePath>
   </parent>
 
@@ -153,7 +153,7 @@
     <dependency>
     	<groupId>org.json</groupId>
     	<artifactId>json</artifactId>
-    	<version>20230227</version>
+    	<version>20231013</version>
     </dependency>
     <dependency>
       <groupId>org.xerial</groupId>