bump mobie-io dependency

mobie · Dec 16, 2023 · 4fb63b7 · 4fb63b7
1 parent efe3261
commit 4fb63b7
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Showing 4 changed files with 4 additions and 11 deletions.
diff --git a/pom.xml b/pom.xml
@@ -85,7 +85,7 @@
 
         <bigdataviewer-playground.version>0.8.0</bigdataviewer-playground.version>
         <imagej-utils.version>0.6.9</imagej-utils.version>
-        <mobie-io.version>2.2.3-SNAPSHOT</mobie-io.version>
+        <mobie-io.version>2.2.3</mobie-io.version>
         <trove.version>1.0.2</trove.version>
         <annotations.version>16.0.2</annotations.version>
 
@@ -105,9 +105,6 @@
         <tablesaw-core.version>0.43.1</tablesaw-core.version>
         <tablesaw-parquet.version>0.10.0</tablesaw-parquet.version>
 
-        <!-- AutoMicTools -->
-        <AutoMicoTools_.version>1.1.66-SNAPSHOT</AutoMicoTools_.version>
-
         <!-- NB: Deploy releases to the SciJava Maven repository. -->
         <releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
 

diff --git a/src/main/java/org/embl/mobie/lib/hcs/Plate.java b/src/main/java/org/embl/mobie/lib/hcs/Plate.java
@@ -119,6 +119,7 @@ public Plate( String hcsDirectory ) throws IOException
 			{
 				imageDataFormat = ImageDataFormat.BioFormatsS3;
 				imageSitePaths = S3Utils.getS3FilePaths( hcsDirectory );
+				ThreadHelper.setNumIoThreads( Math.max( 16, ThreadHelper.getNumIoThreads() ) );
 			}
 			else
 			{

diff --git a/src/main/java/org/embl/mobie/lib/hcs/VirtualBioFormatsStack.java b/src/main/java/org/embl/mobie/lib/hcs/VirtualBioFormatsStack.java
@@ -187,13 +187,7 @@ public ImageProcessor getProcessor(int n) {
         }
         n = translate(n);  // update n for hyperstacks not in the default CZT order
         String path = getFileName( n );
-        ImagePlus imp;
-        // FIXME: Do the resourceTyping in IOHelper!
-        IOHelper.ResourceType resourceType = IOHelper.getType( path );
-        if ( resourceType.equals( IOHelper.ResourceType.S3 ) )
-            imp = IOHelper.openWithBioformatsFromS3( path, 0 );
-        else
-            imp = IOHelper.openWithBioFormats( path, 0);
+        ImagePlus imp = IOHelper.openWithBioFormats( path, 0 );
         ImageProcessor ip = null;
         int depthThisImage = 0;
         if (imp!=null) {

diff --git a/src/test/java/develop/hcs/HCSIncuyteRaw.java b/src/test/java/develop/hcs/HCSIncuyteRaw.java
@@ -32,6 +32,7 @@
 import net.imagej.ImageJ;
 import org.embl.mobie.MoBIE;
 import org.embl.mobie.MoBIESettings;
+import org.embl.mobie.lib.ThreadHelper;
 
 import java.io.IOException;