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Fix series assignment for multiseries files #46

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Fix series assignment for multiseries files #46

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eac9d3d
Fixed setting series for multi-series file
yoda-vid Aug 10, 2017
73e08e3
small change to use series value since used to set series index in Im…
yoda-vid Aug 13, 2017
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1 change: 1 addition & 0 deletions src/main/java/mpicbg/stitching/ImageCollectionElement.java
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Original file line number Diff line number Diff line change
Expand Up @@ -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 );
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6 changes: 3 additions & 3 deletions src/main/java/plugin/Stitching_Grid.java
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Expand Up @@ -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 );
Expand Down Expand Up @@ -956,14 +956,14 @@ 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 );
}
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 );
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