Merge pull request #161 from JaneliaSciComp/splitCorr

Changes in BigStitcher to adapt to splitcorr branch merge

Author: StephanPreibisch

pom.xml

@@ -120,7 +120,7 @@
 		<n5-zarr-version>1.5.0</n5-zarr-version>
 		-->
 
-		<multiview-reconstruction.version>7.0.7</multiview-reconstruction.version>
+		<multiview-reconstruction.version>8.1.1</multiview-reconstruction.version>
 
 		<bigdataviewer-n5.version>1.0.2</bigdataviewer-n5.version>
 		<mpicbg.mpicbg.version>1.6.5</mpicbg.mpicbg.version>

src/main/java/net/preibisch/stitcher/algorithm/globalopt/ExecuteGlobalOpt.java

@@ -76,7 +76,7 @@ public void run()
 			}
 
 			final boolean isSavedFaG = savedFiltering != null;
-			final GlobalOptimizationParameters params = expertMode ? GlobalOptimizationParameters.askUserForParameters(!isSavedFaG) : GlobalOptimizationParameters.askUserForSimpleParameters();
+			final GlobalOptimizationParameters params = GlobalOptimizationParameters.askUserForSimpleParameters();
 			if ( params == null )
 				return;
 

src/main/java/net/preibisch/stitcher/algorithm/globalopt/GlobalOptStitcher.java

@@ -191,6 +191,7 @@ public List< ViewId > getDefaultFixedViews()
 			{
 				HashMap< ViewId, mpicbg.models.Tile< TranslationModel3D > > globalOptResults = GlobalOptTwoRound.computeTiles(
 						new TranslationModel3D(),
+						true,// preAlign
 						new ImageCorrelationPointMatchCreator( results ),
 						new SimpleIterativeConvergenceStrategy( Double.MAX_VALUE,
 								params.relativeThreshold, params.absoluteThreshold ),
@@ -222,6 +223,7 @@ else if ( params.method == GlobalOptType.ONE_ROUND_ITERATIVE)
 			{
 				HashMap< ViewId, mpicbg.models.Tile< TranslationModel3D > > globalOptResults = GlobalOptIterative.computeTiles(
 						new TranslationModel3D(),
+						true,// preAlign
 						new ImageCorrelationPointMatchCreator( results ),
 						new SimpleIterativeConvergenceStrategy( Double.MAX_VALUE,
 								params.relativeThreshold, params.absoluteThreshold ),
@@ -246,6 +248,7 @@ else if ( params.method == GlobalOptType.ONE_ROUND_ITERATIVE)
 			{
 				final HashMap< ViewId, mpicbg.models.Tile< TranslationModel3D > > globalOptResults = GlobalOpt.computeTiles(
 						new TranslationModel3D(),
+						true,// preAlign
 						new ImageCorrelationPointMatchCreator( results ),
 						new SimpleIterativeConvergenceStrategy( Double.MAX_VALUE,
 								params.relativeThreshold, params.absoluteThreshold ),

src/main/java/net/preibisch/stitcher/algorithm/globalopt/TransformationTools.java

@@ -750,6 +750,7 @@ public static void main( String[] args )
 
 		GlobalOpt.computeTiles( 
 				new TranslationModel3D(),
+				true,// preAlign
 				new ImageCorrelationPointMatchCreator( results, 0.5 ),
 				new ConvergenceStrategy( 5.0 ),
 				fixedViews,

src/main/java/net/preibisch/stitcher/gui/StitchingExplorerPanel.java

@@ -265,6 +265,15 @@ public boolean illumsGrouped()
 			return true;
 	}
 
+	@Override
+	protected void clearGroupingCheckboxes()
+	{
+		if ( checkboxGroupChannels != null )
+			checkboxGroupChannels.setSelected( false );
+		if ( checkboxGroupIllums != null )
+			checkboxGroupIllums.setSelected( false );
+	}
+
 
 
 	void quitLinkExplorer()

src/main/java/net/preibisch/stitcher/gui/popup/CalculatePCPopupExpertBatch.java

@@ -31,10 +31,10 @@
 public class CalculatePCPopupExpertBatch extends JMenu implements ExplorerWindowSetable
 {
 
+	private static final long serialVersionUID = 804355154792175254L;
 	final CalculatePCPopup phaseCorrSimple;
 	final CalculatePCPopup phaseCorr;
 	final CalculatePCPopup lucasKanade;
-	final PairwiseInterestPointRegistrationPopup interestPoint;
 	boolean wizardMode;
 
 	public CalculatePCPopupExpertBatch( String description, boolean wizardMode )
@@ -50,13 +50,11 @@ public CalculatePCPopupExpertBatch( String description, boolean wizardMode )
 
 		phaseCorr = new CalculatePCPopup( wizardMode ? "Phase Correlation" : "Phase Correlation (expert)", false, Method.PHASECORRELATION, wizardMode );
 		lucasKanade = new CalculatePCPopup( "Lucas-Kanade", false, Method.LUCASKANADE, wizardMode );
-		interestPoint = new PairwiseInterestPointRegistrationPopup( "Interest point based", wizardMode );
 
 		if(!wizardMode)
 			this.add(phaseCorrSimple);
 		this.add( phaseCorr );
 		this.add( lucasKanade );
-		this.add( interestPoint );
 	}
 
 	@Override
@@ -66,7 +64,6 @@ public JComponent setExplorerWindow( ExplorerWindow< ? > panel )
 			this.phaseCorrSimple.setExplorerWindow( panel );
 		this.phaseCorr.setExplorerWindow( panel );
 		this.lucasKanade.setExplorerWindow( panel );
-		this.interestPoint.setExplorerWindow( panel );
 		return this;
 	}
 

src/main/java/net/preibisch/stitcher/gui/popup/PairwiseInterestPointRegistrationPopup.java

@@ -32,6 +32,7 @@
 
 import net.preibisch.legacy.io.IOFunctions;
 import net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters;
+import net.preibisch.mvrecon.fiji.plugin.interestpointregistration.global.GlobalOptimizationParameters.PreAlign;
 import net.preibisch.mvrecon.fiji.plugin.util.MouseOverPopUpStateChanger;
 import net.preibisch.mvrecon.fiji.plugin.util.MouseOverPopUpStateChanger.StateChanger;
 import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
@@ -243,7 +244,7 @@ public void actionPerformed( ActionEvent e )
 					if ( !ICPRefinement.getGUIParametersSimple( icpType, data, params, downsamplingChoice, thresholdChoice, distanceChoice ) )
 						return;
 
-					globalOptParams = GlobalOptimizationParameters.getGlobalOptimizationParametersForSelection( GlobalOptimizationParameters.defaultSimple );
+					globalOptParams = GlobalOptimizationParameters.getGlobalOptimizationParametersForSelection( GlobalOptimizationParameters.defaultSimple, false );
 				}
 
 				if ( globalOptParams == null )

src/main/java/net/preibisch/stitcher/gui/popup/RefineWithICPPopup.java

@@ -148,6 +148,7 @@ public static void main( String[] args )
 
 		final HashMap< ViewId, TranslationModel3D > computeResults = GlobalOptTwoRound.computeModels(
 				new TranslationModel3D(),
+				true,// preAlign
 				pmc,
 				cs,
 				new MaxErrorLinkRemoval(),