diff --git a/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java b/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java index d20bb2a7a57c501762a7162f8a62d11444cc4b7b..7b1e2e514c86ddc68ab337bd9c91ad630e3ce673 100644 --- a/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java +++ b/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java @@ -709,6 +709,10 @@ public class ExportSpimSequencePlugIn implements PlugIn public static void main( final String[] args ) { + Bead_Registration.spimDataDirectory = "/Users/pietzsch/workspace/data/openspim"; + Bead_Registration.fileNamePattern = "spim_TL{tt}_Angle{a}.tif"; + Bead_Registration.timepoints = "0"; + Bead_Registration.angles = "0"; new ExportSpimSequencePlugIn().run( null ); } } diff --git a/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java b/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java index f252d7ee50294fa6a20624a534dc29365b4e416b..4f47291cba977c3eb71a9b69c3b57a99728cd3be 100644 --- a/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java +++ b/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java @@ -1,7 +1,7 @@ package bdv.ij.export.imgloader; -import ij.IJ; import ij.ImagePlus; +import io.scif.SCIFIOService; import io.scif.img.ImgIOException; import io.scif.img.ImgOpener; @@ -21,6 +21,10 @@ import net.imglib2.meta.ImgPlus; import net.imglib2.type.numeric.integer.UnsignedByteType; import net.imglib2.type.numeric.integer.UnsignedShortType; +import org.scijava.Context; +import org.scijava.app.AppService; +import org.scijava.app.StatusService; + /** * This {@link ImgLoader} loads images that represent a 3D stack in a single @@ -33,7 +37,7 @@ import net.imglib2.type.numeric.integer.UnsignedShortType; */ public class StackImageLoader implements BasicImgLoader< UnsignedShortType > { - private ImgOpener opener; + private final ImgOpener opener; private final ArrayImgFactory< UnsignedShortType > factory; @@ -47,14 +51,7 @@ public class StackImageLoader implements BasicImgLoader< UnsignedShortType > { this.filenames = filenames; this.useImageJOpener = useImageJOpener; - try - { - opener = new ImgOpener(); - } - catch ( final Exception e ) - { - e.printStackTrace(); - } + opener = useImageJOpener ? null : new ImgOpener( new Context( SCIFIOService.class, AppService.class, StatusService.class ) ); factory = new ArrayImgFactory< UnsignedShortType >(); type = new UnsignedShortType(); } @@ -65,11 +62,6 @@ public class StackImageLoader implements BasicImgLoader< UnsignedShortType > final String fn = filenames.get( view ); if ( useImageJOpener ) { - if ( opener == null ) - { - IJ.showMessage( "Error", "Error: Could not create io.scif.img.ImgOpener" ); - return null; - } final ImagePlus imp = new ImagePlus( fn ); if ( imp.getType() == ImagePlus.GRAY16 ) return new ImgPlus< UnsignedShortType >( ImageJFunctions.wrapShort( imp ) );