Merge pull request #60 from melissalinkert/uint32

Add uint32 support
glencoesoftware · Sep 29, 2020 · 070ba9a · 070ba9a
2 parents 65c806a + 41b0743
commit 070ba9a
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Showing 3 changed files with 125 additions and 127 deletions.
diff --git a/build.gradle b/build.gradle
@@ -30,19 +30,22 @@ dependencies {
     implementation 'info.picocli:picocli:4.2.0'
     implementation 'com.univocity:univocity-parsers:2.8.4'
     implementation 'org.janelia.saalfeldlab:n5:2.2.0'
-    implementation 'org.janelia.saalfeldlab:n5-blosc:1.1.0'
-    implementation 'org.janelia.saalfeldlab:n5-zarr:0.0.4'
+
+    // exclude JUnit 4 to make sure our tests all use JUnit 5
+    implementation('org.janelia.saalfeldlab:n5-blosc:1.1.0') {
+        exclude group: 'junit', module: 'junit'
+    }
+    implementation('org.janelia.saalfeldlab:n5-zarr:0.0.4') {
+        exclude group: 'junit', module: 'junit'
+    }
     implementation 'org.openpnp:opencv:3.4.2-1'
 
     // https://github.com/junit-team/junit5-samples/blob/master/junit5-migration-gradle/build.gradle
-    def junit4Version        = '4.12'
-    def junitVintageVersion  = '5.2.0'
-    def junitJupiterVersion  = '5.2.0'
-    def junitPlatformVersion = '1.2.0'
+    def junitVintageVersion  = '5.7.0'
+    def junitJupiterVersion  = '5.7.0'
+    def junitPlatformVersion = '1.7.0'
     testImplementation "org.junit.jupiter:junit-jupiter-api:${junitJupiterVersion}"
     testRuntimeOnly "org.junit.jupiter:junit-jupiter-engine:${junitJupiterVersion}"
-    testImplementation "junit:junit:${junit4Version}"
-    testRuntimeOnly "org.junit.vintage:junit-vintage-engine:${junitVintageVersion}"
     testRuntimeOnly "org.junit.platform:junit-platform-launcher:${junitPlatformVersion}"
 
     // https://stackoverflow.com/questions/45462987/junit5-with-intellij-and-gradle
@@ -58,6 +61,10 @@ jar {
     }
 }
 
+test {
+    useJUnitPlatform()
+}
+
 distributions {
     main {
         contents {

diff --git a/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java b/src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
@@ -63,6 +63,7 @@
 import org.janelia.saalfeldlab.n5.DoubleArrayDataBlock;
 import org.janelia.saalfeldlab.n5.FloatArrayDataBlock;
 import org.janelia.saalfeldlab.n5.GzipCompression;
+import org.janelia.saalfeldlab.n5.IntArrayDataBlock;
 import org.janelia.saalfeldlab.n5.Lz4Compression;
 import org.janelia.saalfeldlab.n5.N5FSReader;
 import org.janelia.saalfeldlab.n5.N5FSWriter;
@@ -877,6 +878,13 @@ private void processTile(
           dataBlock = new ShortArrayDataBlock(size, gridPosition, asShort);
           break;
         }
+        case FormatTools.INT32:
+        case FormatTools.UINT32: {
+          int[] asInt = new int[tile.length / 4];
+          bb.asIntBuffer().get(asInt);
+          dataBlock = new IntArrayDataBlock(size, gridPosition, asInt);
+          break;
+        }
         case FormatTools.FLOAT: {
           float[] asFloat = new float[tile.length / 4];
           bb.asFloatBuffer().get(asFloat);
@@ -979,6 +987,12 @@ public void saveResolutions(int series)
       case FormatTools.UINT16:
         dataType = DataType.UINT16;
         break;
+      case FormatTools.INT32:
+        dataType = DataType.INT32;
+        break;
+      case FormatTools.UINT32:
+        dataType = DataType.UINT32;
+        break;
       case FormatTools.FLOAT:
         dataType = DataType.FLOAT32;
         break;