From 160cc1d630e171dbef4660ded8863b017089d512 Mon Sep 17 00:00:00 2001
From: Tobias Pietzsch <tobias.pietzsch@gmail.com>
Date: Fri, 22 Aug 2014 16:14:29 +0200
Subject: [PATCH] contruct ImgOpener with a Context that works (for now) in
both Eclipse and Fiji
---
.../java/bdv/ij/ExportSpimSequencePlugIn.java | 4 ++++
.../ij/export/imgloader/StackImageLoader.java | 22 ++++++-------------
2 files changed, 11 insertions(+), 15 deletions(-)
diff --git a/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java b/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java
index d20bb2a..7b1e2e5 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 f252d7e..4f47291 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 ) );
--
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