From eac9d3d66ec6a9ee570d014f3817edb69eb0cfdd Mon Sep 17 00:00:00 2001 From: David Young Date: Thu, 10 Aug 2017 16:26:17 -0700 Subject: [PATCH 1/2] Fixed setting series for multi-series file --- src/main/java/mpicbg/stitching/ImageCollectionElement.java | 1 + src/main/java/plugin/Stitching_Grid.java | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/main/java/mpicbg/stitching/ImageCollectionElement.java b/src/main/java/mpicbg/stitching/ImageCollectionElement.java index 0b47ce7..9f4a5f2 100644 --- a/src/main/java/mpicbg/stitching/ImageCollectionElement.java +++ b/src/main/java/mpicbg/stitching/ImageCollectionElement.java @@ -109,6 +109,7 @@ public ImagePlus open( final boolean virtual ) ImporterOptions options = new ImporterOptions(); options.setId( file.getAbsolutePath() ); + options.setSeriesOn(getIndex(), true); options.setSplitChannels( false ); options.setSplitTimepoints( false ); options.setSplitFocalPlanes( false ); diff --git a/src/main/java/plugin/Stitching_Grid.java b/src/main/java/plugin/Stitching_Grid.java index 3515279..3ef4704 100644 --- a/src/main/java/plugin/Stitching_Grid.java +++ b/src/main/java/plugin/Stitching_Grid.java @@ -892,7 +892,7 @@ protected ArrayList< ImageCollectionElement > getLayoutFromMultiSeriesFile( fina // CTR HACK: In the case of a single series, we treat each time point // as a separate series for the purpose of stitching tiles. timeHack = numSeries == 1; - + for ( int series = 0; series < numSeries; ++series ) { Log.debug( "fetching data for series: " + series ); @@ -963,7 +963,7 @@ protected ArrayList< ImageCollectionElement > getLayoutFromMultiSeriesFile( fina } else { - element = new ImageCollectionElement( new File( multiSeriesFile ), elements.size() ); + element = new ImageCollectionElement( new File( multiSeriesFile ), series ); element.setModel( new TranslationModel3D() ); element.setOffset( new float[]{ (float)locationX, (float)locationY, (float)locationZ } ); element.setDimensionality( 3 ); From 73e08e313ef52a386983aa64b3947c6e2786a3b5 Mon Sep 17 00:00:00 2001 From: David Young Date: Sun, 13 Aug 2017 15:57:41 -0700 Subject: [PATCH 2/2] small change to use series value since used to set series index in ImageCollectionElement --- src/main/java/plugin/Stitching_Grid.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/plugin/Stitching_Grid.java b/src/main/java/plugin/Stitching_Grid.java index 3ef4704..d1640d9 100644 --- a/src/main/java/plugin/Stitching_Grid.java +++ b/src/main/java/plugin/Stitching_Grid.java @@ -956,7 +956,7 @@ protected ArrayList< ImageCollectionElement > getLayoutFromMultiSeriesFile( fina if ( dim == 2 ) { - element = new ImageCollectionElement( new File( multiSeriesFile ), elements.size() ); + element = new ImageCollectionElement( new File( multiSeriesFile ), series ); element.setModel( new TranslationModel2D() ); element.setOffset( new float[]{ (float)locationX, (float)locationY } ); element.setDimensionality( 2 );