From ab592b44344925bf4bc97e1a4c6b019df163adf5 Mon Sep 17 00:00:00 2001
From: Tobias Pietzsch <tobias.pietzsch@gmail.com>
Date: Wed, 5 Oct 2016 13:26:34 +0200
Subject: [PATCH] fix uses of deprecated bigdataviewer and imglib2 API
---
src/main/java/bdv/ij/BigDataBrowserPlugIn.java | 4 +++-
src/main/java/bdv/ij/BigDataViewerPlugIn.java | 8 ++++----
src/main/java/bdv/ij/OpenImarisPlugIn.java | 10 +++++-----
.../java/bdv/ij/export/SpimRegistrationSequence.java | 9 +++++++--
4 files changed, 19 insertions(+), 12 deletions(-)
diff --git a/src/main/java/bdv/ij/BigDataBrowserPlugIn.java b/src/main/java/bdv/ij/BigDataBrowserPlugIn.java
index 808896c..76d6b12 100644
--- a/src/main/java/bdv/ij/BigDataBrowserPlugIn.java
+++ b/src/main/java/bdv/ij/BigDataBrowserPlugIn.java
@@ -150,7 +150,9 @@ public class BigDataBrowserPlugIn implements PlugIn
System.out.println( key );
try
{
- BigDataViewer.view( datasetUrlMap.get( key ), new ProgressWriterIJ() );
+ final String filename = datasetUrlMap.get( key );
+ final String title = new File( filename ).getName();
+ BigDataViewer.open( filename, title, new ProgressWriterIJ(), ViewerOptions.options() );
}
catch ( final SpimDataException e )
{
diff --git a/src/main/java/bdv/ij/BigDataViewerPlugIn.java b/src/main/java/bdv/ij/BigDataViewerPlugIn.java
index 0e26d3b..0267908 100644
--- a/src/main/java/bdv/ij/BigDataViewerPlugIn.java
+++ b/src/main/java/bdv/ij/BigDataViewerPlugIn.java
@@ -1,8 +1,5 @@
package bdv.ij;
-import ij.Prefs;
-import ij.plugin.PlugIn;
-
import java.awt.FileDialog;
import java.awt.Frame;
import java.io.File;
@@ -15,6 +12,9 @@ import javax.swing.filechooser.FileFilter;
import bdv.BigDataViewer;
import bdv.ij.util.ProgressWriterIJ;
+import bdv.viewer.ViewerOptions;
+import ij.Prefs;
+import ij.plugin.PlugIn;
public class BigDataViewerPlugIn implements PlugIn
{
@@ -105,7 +105,7 @@ public class BigDataViewerPlugIn implements PlugIn
try
{
lastDatasetPath = file.getAbsolutePath();
- BigDataViewer.view( file.getAbsolutePath(), new ProgressWriterIJ() );
+ BigDataViewer.open( file.getAbsolutePath(), file.getName(), new ProgressWriterIJ(), ViewerOptions.options() );
}
catch ( final Exception e )
{
diff --git a/src/main/java/bdv/ij/OpenImarisPlugIn.java b/src/main/java/bdv/ij/OpenImarisPlugIn.java
index dafc4be..0e1d450 100644
--- a/src/main/java/bdv/ij/OpenImarisPlugIn.java
+++ b/src/main/java/bdv/ij/OpenImarisPlugIn.java
@@ -1,9 +1,5 @@
package bdv.ij;
-import ij.ImageJ;
-import ij.Prefs;
-import ij.plugin.PlugIn;
-
import java.awt.FileDialog;
import java.awt.Frame;
import java.io.File;
@@ -18,6 +14,10 @@ import bdv.BigDataViewer;
import bdv.ij.util.ProgressWriterIJ;
import bdv.img.imaris.Imaris;
import bdv.spimdata.SpimDataMinimal;
+import bdv.viewer.ViewerOptions;
+import ij.ImageJ;
+import ij.Prefs;
+import ij.plugin.PlugIn;
public class OpenImarisPlugIn implements PlugIn
{
@@ -114,7 +114,7 @@ public class OpenImarisPlugIn implements PlugIn
{
lastDatasetPath = file.getAbsolutePath();
final SpimDataMinimal spimData = Imaris.openIms( file.getAbsolutePath() );
- new BigDataViewer( spimData, file.getName(), new ProgressWriterIJ() );
+ BigDataViewer.open( spimData, file.getName(), new ProgressWriterIJ(), ViewerOptions.options() );
}
catch ( final IOException e )
{
diff --git a/src/main/java/bdv/ij/export/SpimRegistrationSequence.java b/src/main/java/bdv/ij/export/SpimRegistrationSequence.java
index 5564965..2cd38a7 100644
--- a/src/main/java/bdv/ij/export/SpimRegistrationSequence.java
+++ b/src/main/java/bdv/ij/export/SpimRegistrationSequence.java
@@ -328,8 +328,13 @@ public class SpimRegistrationSequence
else
imgD = conf.cropSizeZ/scale;
- // TODO: this should be a RealInterval
- return FinalRealInterval.createMinSize( ( int ) min.x + cropOffsetX, (int ) min.y + cropOffsetY, ( int ) min.z + cropOffsetZ, imgW, imgH, imgD );
+ return FinalRealInterval.createMinMax(
+ ( int ) min.x + cropOffsetX,
+ ( int ) min.y + cropOffsetY,
+ ( int ) min.z + cropOffsetZ,
+ ( int ) min.x + cropOffsetX + imgW - 1,
+ ( int ) min.y + cropOffsetY + imgH - 1,
+ ( int ) min.z + cropOffsetZ + imgD - 1 );
}
protected static ViewRegistrations createViewRegistrations( final SPIMConfiguration conf, final ArrayList< ViewSetup > setups )
--
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