diff --git a/src/main/java/bdv/ij/BigDataBrowserPlugIn.java b/src/main/java/bdv/ij/BigDataBrowserPlugIn.java index 808896c200bd37c64ce20697acd40ee3a736b432..76d6b12aabf2cfec6eeda6bc87344fd6149e8035 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 0e26d3b5b5bd5cb873dae46d8193b5a15a016916..0267908e864b632a171afa12ac990946095e5917 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 dafc4be70026e64a6b1ca8037dbc7c748477eda3..0e1d4507df30030e16f499cf170d02c27866eb2e 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 55649650811640a44e3311fe8956a41c883bf5b4..2cd38a75548f878224bdec7608883e7509d6b982 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 )