diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml index 6ccd5fe3..5f8e99dc 100644 --- a/dependency-reduced-pom.xml +++ b/dependency-reduced-pom.xml @@ -10,7 +10,7 @@ org.embl.mobie mobie-io MoBIE IO - 2.2.1 + 2.2.2-SNAPSHOT Readers and writers for image data in MoBIE projects https://github.com/mobie/mobie-io @@ -83,7 +83,6 @@ scm:git:https://github.com/mobie/mobie-io scm:git:git@github.com:mobie/mobie-io - mobie-io-2.2.1 https://github.com/mobie/mobie-io diff --git a/pom.xml b/pom.xml index ca1f515f..1a1ef8a2 100644 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.scijava pom-scijava - 37.0.0 + 36.0.0 org.embl.mobie diff --git a/src/main/java/org/embl/mobie/io/ImageDataFormat.java b/src/main/java/org/embl/mobie/io/ImageDataFormat.java index 6d4472c2..c8d9425c 100644 --- a/src/main/java/org/embl/mobie/io/ImageDataFormat.java +++ b/src/main/java/org/embl/mobie/io/ImageDataFormat.java @@ -203,7 +203,7 @@ public static ImageDataFormat fromPath(String path) return ImageDataFormat.OmeZarr; else if (lowerCase.endsWith( ".xml" )) return ImageDataFormat.Bdv; // TODO: https://github.com/mobie/mobie-io/issues/131 - else if (lowerCase.endsWith( ".ome.tif" ) || lowerCase.endsWith( ".ome.tiff" )) + else if (lowerCase.endsWith( ".ome.tif" ) || lowerCase.endsWith( ".ome.tiff" ) ) return ImageDataFormat.BioFormats; else if (lowerCase.endsWith( ".tif" ) || lowerCase.endsWith( ".tiff" )) return ImageDataFormat.Tiff; @@ -212,7 +212,7 @@ else if (lowerCase.endsWith( ".h5" )) else if (lowerCase.endsWith( ".toml" )) return ImageDataFormat.Toml; else - return ImageDataFormat.ImageJ; + return ImageDataFormat.BioFormats; } public boolean inMemory() diff --git a/src/main/java/org/embl/mobie/io/SpimDataOpener.java b/src/main/java/org/embl/mobie/io/SpimDataOpener.java index 2db7a3f5..e8f61793 100644 --- a/src/main/java/org/embl/mobie/io/SpimDataOpener.java +++ b/src/main/java/org/embl/mobie/io/SpimDataOpener.java @@ -128,7 +128,12 @@ public SpimDataOpener() { case Tiff: return open(IOHelper.openTiffAsImagePlus( imagePath ), sharedQueue); case ImageJ: - return open(IJ.openImage(imagePath), sharedQueue); + ImagePlus imagePlus = IJ.openImage( imagePath ); + if ( imagePlus == null ) + { + throw new RuntimeException("Could not open " + imagePath ); + } + return open( imagePlus, sharedQueue); case BioFormats: return openWithBioFormats(imagePath, sharedQueue); case BdvN5: @@ -301,9 +306,7 @@ private SpimData openBdvOmeZarrS3(String path, SharedQueue queue) { public AbstractSpimData< ? > openWithBioFormats( String path, SharedQueue sharedQueue ) { final AbstractSpimData< ? > spimData = openWithBioFormats( path ); - setSharedQueue( sharedQueue, spimData ); - return spimData; }