From 166e3b21f7493b2c939a70a1b5c021d589c2507d Mon Sep 17 00:00:00 2001 From: Stephan Preibisch Date: Fri, 3 Nov 2023 09:19:08 -0400 Subject: [PATCH 01/13] use pom-scijava 37.0.0 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index e9976c852..b607a95e8 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ org.scijava pom-scijava - 36.0.0 + 37.0.0 From e10dc99d0722b9f72606c426c06bf8aeb57bd77a Mon Sep 17 00:00:00 2001 From: Stephan Preibisch Date: Fri, 3 Nov 2023 09:21:47 -0400 Subject: [PATCH 02/13] Bump to next development cycle Signed-off-by: Stephan Preibisch --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index b607a95e8..faacb112c 100644 --- a/pom.xml +++ b/pom.xml @@ -11,7 +11,7 @@ net.preibisch multiview-reconstruction - 3.2.4-SNAPSHOT + 3.2.5-SNAPSHOT Multiview Reconstruction Software for the reconstruction of multi-view microscopic acquisitions From 14e903bfb9a491d85706f8530548b0145bd0089e Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Fri, 3 Nov 2023 14:14:59 +0100 Subject: [PATCH 03/13] POM: bump to pom-scijava-37.0.0, bump to bigdataviewer-core-10.4.12 --- pom.xml | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/pom.xml b/pom.xml index e9976c852..ddb91fa14 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ org.scijava pom-scijava - 36.0.0 + 37.0.0 @@ -105,12 +105,8 @@ like Selective Plane Illumination Microscopy (SPIM) Data. sign,deploy-to-scijava - 6.1.0 - 0.13.2 - 1.0.0-beta-17 - 10.4.6 - 1.0.0-beta-32 - 5.0.0 + 10.4.12 + 1.0.0-beta-33 From bedf81c5d1b5b2a055522d387ddbc2d9a793ed25 Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Fri, 3 Nov 2023 22:52:42 +0100 Subject: [PATCH 04/13] fix overridden method signature --- .../mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java index 83219fc2f..93d835ccf 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java @@ -78,7 +78,7 @@ public BDVPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? >, ? > panel ) { this.panel = panel; return this; From af042836c6167c948318a2f3524444d8e425ee39 Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Mon, 6 Nov 2023 21:02:10 +0100 Subject: [PATCH 05/13] Remove unnecessary generics --- .../popup/ApplyTransformationPopup.java | 14 ++++++------- .../spimdata/explorer/popup/BDVPopup.java | 2 +- .../popup/BakeManualTransformationPopup.java | 7 +------ .../explorer/popup/ExplorerWindowSetable.java | 2 +- .../popup/FlatFieldCorrectionPopup.java | 7 ++----- .../explorer/popup/MaxProjectPopup.java | 4 ++-- .../explorer/popup/ReorientSamplePopup.java | 6 ++---- .../spimdata/explorer/popup/ResavePopup.java | 20 ++----------------- .../explorer/popup/SimpleHyperlinkPopup.java | 6 +----- .../popup/SpecifyCalibrationPopup.java | 4 ++-- .../popup/VisualizeDetectionsPopup.java | 6 ++---- .../explorer/popup/VisualizeNonRigid.java | 4 ++-- 12 files changed, 24 insertions(+), 58 deletions(-) diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ApplyTransformationPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ApplyTransformationPopup.java index 4803b86ee..274a2c97f 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ApplyTransformationPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ApplyTransformationPopup.java @@ -39,8 +39,6 @@ import net.preibisch.mvrecon.fiji.spimdata.explorer.GroupedRowWindow; import mpicbg.spim.data.SpimData; -import mpicbg.spim.data.generic.AbstractSpimData; -import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; import mpicbg.spim.data.sequence.ViewDescription; import mpicbg.spim.data.sequence.ViewId; @@ -49,7 +47,7 @@ public class ApplyTransformationPopup extends JMenuItem implements ExplorerWindo private static final long serialVersionUID = 5234649267634013390L; public static boolean showWarning = true; - ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel; + ExplorerWindow< ?, ? > panel; public ApplyTransformationPopup() { @@ -59,20 +57,20 @@ public ApplyTransformationPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) { this.panel = panel; return this; } - public static final List< ViewId > getSelectedViews( - final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel) + public static final List< ViewId > getSelectedViews( final ExplorerWindow< ?, ? > panel ) { return getSelectedViews( panel, true ); } + public static final List< ViewId > getSelectedViews( - final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel, - final boolean filterMissing) + final ExplorerWindow< ?, ? > panel, + final boolean filterMissing ) { final List< ViewId > viewIds = new ArrayList<>(); if (GroupedRowWindow.class.isInstance( panel )) diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java index 93d835ccf..83219fc2f 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java @@ -78,7 +78,7 @@ public BDVPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? >, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BakeManualTransformationPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BakeManualTransformationPopup.java index ac18e7180..95eb9e57c 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BakeManualTransformationPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BakeManualTransformationPopup.java @@ -24,7 +24,6 @@ import java.awt.event.ActionEvent; import java.util.ArrayList; -import java.util.List; import javax.swing.JComponent; import javax.swing.JMenuItem; @@ -33,8 +32,6 @@ import bdv.tools.transformation.TransformedSource; import bdv.viewer.state.SourceState; import bdv.viewer.state.ViewerState; -import mpicbg.spim.data.generic.AbstractSpimData; -import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; import mpicbg.spim.data.registration.ViewRegistration; import mpicbg.spim.data.registration.ViewRegistrations; import mpicbg.spim.data.registration.ViewTransform; @@ -44,8 +41,6 @@ import net.preibisch.legacy.io.IOFunctions; import net.preibisch.mvrecon.fiji.spimdata.SpimData2; import net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow; -import net.preibisch.mvrecon.fiji.spimdata.explorer.ViewSetupExplorerPanel; -import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group; public class BakeManualTransformationPopup extends JMenuItem implements ExplorerWindowSetable { @@ -61,7 +56,7 @@ public BakeManualTransformationPopup() } @Override - public JComponent setExplorerWindow( ExplorerWindow>, ?> panel ) + public JComponent setExplorerWindow( ExplorerWindow< ?, ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ExplorerWindowSetable.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ExplorerWindowSetable.java index 70829c5e0..52e0e079c 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ExplorerWindowSetable.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ExplorerWindowSetable.java @@ -31,6 +31,6 @@ public interface ExplorerWindowSetable { - public JComponent setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel ); + public JComponent setExplorerWindow( final ExplorerWindow< ?, ? > panel ); } // AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > > diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FlatFieldCorrectionPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FlatFieldCorrectionPopup.java index 6f85b60a8..37a4bcbe0 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FlatFieldCorrectionPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FlatFieldCorrectionPopup.java @@ -35,8 +35,6 @@ import javax.swing.JMenuItem; import fiji.util.gui.GenericDialogPlus; -import mpicbg.spim.data.generic.AbstractSpimData; -import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; import mpicbg.spim.data.sequence.Channel; import mpicbg.spim.data.sequence.Illumination; import mpicbg.spim.data.sequence.ImgLoader; @@ -54,7 +52,7 @@ public class FlatFieldCorrectionPopup extends JMenuItem implements ExplorerWindo { private static final long serialVersionUID = 950277697000203629L; - private ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel; + private ExplorerWindow< ?, ? > panel; public FlatFieldCorrectionPopup() { @@ -63,8 +61,7 @@ public FlatFieldCorrectionPopup() } @Override - public JComponent setExplorerWindow( - ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel) + public JComponent setExplorerWindow( ExplorerWindow< ?, ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/MaxProjectPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/MaxProjectPopup.java index 7481aa420..b71bc6533 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/MaxProjectPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/MaxProjectPopup.java @@ -44,7 +44,7 @@ public class MaxProjectPopup extends JMenuItem implements ExplorerWindowSetable private static final long serialVersionUID = 5234649267634013390L; public static boolean showWarning = true; - ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel; + ExplorerWindow< ?, ? > panel; public MaxProjectPopup() { @@ -54,7 +54,7 @@ public MaxProjectPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ReorientSamplePopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ReorientSamplePopup.java index 2b2221382..0b6b359c9 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ReorientSamplePopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ReorientSamplePopup.java @@ -31,8 +31,6 @@ import bdv.BigDataViewer; import mpicbg.spim.data.SpimData; -import mpicbg.spim.data.generic.AbstractSpimData; -import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; import mpicbg.spim.data.sequence.ViewDescription; import mpicbg.spim.data.sequence.ViewId; import net.imglib2.realtransform.AffineTransform3D; @@ -48,7 +46,7 @@ public class ReorientSamplePopup extends JMenuItem implements ExplorerWindowSeta private static final long serialVersionUID = 5234649267634013390L; public static boolean showWarning = true; - ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel; + ExplorerWindow< ?, ? > panel; public ReorientSamplePopup() { @@ -58,7 +56,7 @@ public ReorientSamplePopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java index 7950f2616..7c2492332 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java @@ -25,10 +25,7 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.io.File; -import java.io.IOException; import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; import java.util.Date; import java.util.List; import java.util.Map; @@ -38,22 +35,11 @@ import javax.swing.JMenuItem; import javax.swing.JOptionPane; -import org.janelia.saalfeldlab.n5.GzipCompression; - import bdv.export.ExportMipmapInfo; import bdv.export.ProgressWriter; -import bdv.export.ProposeMipmaps; -import bdv.export.WriteSequenceToHdf5; -import bdv.export.ExportScalePyramid; -import bdv.export.n5.WriteSequenceToN5; import bdv.img.n5.N5ImageLoader; -import mpicbg.spim.data.generic.AbstractSpimData; -import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; import mpicbg.spim.data.sequence.ViewId; import mpicbg.spim.data.sequence.ViewSetup; -import net.imglib2.img.array.ArrayImgFactory; -import net.imglib2.img.cell.CellImgFactory; -import net.imglib2.type.numeric.real.FloatType; import net.preibisch.legacy.io.IOFunctions; import net.preibisch.mvrecon.fiji.ImgLib2Temp.Pair; import net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5; @@ -66,8 +52,6 @@ import net.preibisch.mvrecon.fiji.spimdata.SpimData2; import net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow; import net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel; -import net.preibisch.mvrecon.fiji.spimdata.imgloaders.AbstractImgFactoryImgLoader; -import net.preibisch.mvrecon.fiji.spimdata.imgloaders.MicroManagerImgLoader; public class ResavePopup extends JMenu implements ExplorerWindowSetable { @@ -102,9 +86,9 @@ public ResavePopup() } @Override - public JMenuItem setExplorerWindow(ExplorerWindow>, ?> panel ) + public JMenuItem setExplorerWindow( ExplorerWindow< ?, ? > panel ) { - this.panel = (FilteredAndGroupedExplorerPanel< ?, ? >)panel; + this.panel = ( FilteredAndGroupedExplorerPanel< ?, ? > ) panel; return this; } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SimpleHyperlinkPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SimpleHyperlinkPopup.java index 77cc021ce..fda8bf482 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SimpleHyperlinkPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SimpleHyperlinkPopup.java @@ -34,10 +34,7 @@ import javax.swing.JLabel; import javax.swing.JMenuItem; -import mpicbg.spim.data.generic.AbstractSpimData; -import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; import net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow; -import net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ExplorerWindowSetable; public class SimpleHyperlinkPopup extends JMenuItem implements ExplorerWindowSetable { @@ -55,8 +52,7 @@ public SimpleHyperlinkPopup(String title, URI uri) } @Override - public JComponent setExplorerWindow( - ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel) + public JComponent setExplorerWindow( ExplorerWindow< ?, ? > panel ) { return this; } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SpecifyCalibrationPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SpecifyCalibrationPopup.java index 6ef51d2db..99e0fcc9e 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SpecifyCalibrationPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SpecifyCalibrationPopup.java @@ -45,7 +45,7 @@ public class SpecifyCalibrationPopup extends JMenuItem implements ExplorerWindow private static final long serialVersionUID = 5234649267634013390L; public static boolean showWarning = true; - ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel; + ExplorerWindow< ?, ? > panel; public SpecifyCalibrationPopup() { @@ -55,7 +55,7 @@ public SpecifyCalibrationPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeDetectionsPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeDetectionsPopup.java index 2fa4892e4..b0bc4b432 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeDetectionsPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeDetectionsPopup.java @@ -34,15 +34,13 @@ import net.preibisch.mvrecon.fiji.spimdata.SpimData2; import net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow; -import mpicbg.spim.data.generic.AbstractSpimData; -import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; import mpicbg.spim.data.sequence.ViewId; public class VisualizeDetectionsPopup extends JMenuItem implements ExplorerWindowSetable { private static final long serialVersionUID = 5234649267634013390L; - ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel; + ExplorerWindow< ?, ? > panel; public VisualizeDetectionsPopup() { @@ -52,7 +50,7 @@ public VisualizeDetectionsPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeNonRigid.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeNonRigid.java index 8c1a36704..647517153 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeNonRigid.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeNonRigid.java @@ -69,7 +69,7 @@ public class VisualizeNonRigid extends JMenuItem implements ExplorerWindowSetabl { private static final long serialVersionUID = -4858927229313796971L; - ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel; + ExplorerWindow< ?, ? > panel; final private static String[] displayOptions = new String[] { "Overlay all views affine vs. non-rigid", @@ -87,7 +87,7 @@ public VisualizeNonRigid() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ? extends AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > >, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) { this.panel = panel; return this; From debcdd4445cc96489d5bd809df642d798e198077 Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Fri, 10 Nov 2023 16:19:26 +0100 Subject: [PATCH 06/13] Fix usage of deprecated API in BDVPopup --- .../spimdata/explorer/popup/BDVPopup.java | 315 +++++++----------- 1 file changed, 129 insertions(+), 186 deletions(-) diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java index 83219fc2f..8f7d01d7f 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java @@ -9,12 +9,12 @@ * it under the terms of the GNU General Public License as * published by the Free Software Foundation, either version 2 of the * License, or (at your option) any later version. - * + * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. - * + * * You should have received a copy of the GNU General Public * License along with this program. If not, see * . @@ -22,12 +22,16 @@ */ package net.preibisch.mvrecon.fiji.spimdata.explorer.popup; +import bdv.tools.brightness.ConverterSetup; +import bdv.util.Bounds; +import bdv.viewer.ConverterSetups; +import bdv.viewer.SourceAndConverter; +import bdv.viewer.ViewerFrame; +import bdv.viewer.ViewerState; import java.awt.Dimension; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.lang.reflect.Field; -import java.lang.reflect.Method; -import java.util.List; +import java.util.Collection; import javax.swing.JMenuItem; import javax.swing.JOptionPane; @@ -35,14 +39,10 @@ import bdv.AbstractSpimSource; import bdv.BigDataViewer; import bdv.tools.InitializeViewerState; -import bdv.tools.brightness.MinMaxGroup; -import bdv.tools.brightness.SetupAssignments; import bdv.tools.transformation.TransformedSource; import bdv.viewer.Source; import bdv.viewer.ViewerOptions; import bdv.viewer.ViewerPanel; -import bdv.viewer.state.SourceState; -import bdv.viewer.state.ViewerState; import mpicbg.spim.data.generic.AbstractSpimData; import mpicbg.spim.data.registration.ViewRegistration; import net.imglib2.Interval; @@ -52,6 +52,9 @@ import net.imglib2.histogram.Real1dBinMapper; import net.imglib2.realtransform.AffineTransform3D; import net.imglib2.type.numeric.RealType; +import net.imglib2.type.numeric.integer.UnsignedByteType; +import net.imglib2.type.numeric.integer.UnsignedShortType; +import net.imglib2.util.Cast; import net.imglib2.util.LinAlgHelpers; import net.imglib2.view.Views; import net.preibisch.legacy.io.IOFunctions; @@ -84,6 +87,7 @@ public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) return this; } + // TODO (TP): replace with method and method reference public class MyActionListener implements ActionListener { @Override @@ -95,6 +99,7 @@ public void actionPerformed( final ActionEvent e ) return; } + // TODO (TP): replace with lambda new Thread( new Runnable() { @Override @@ -144,53 +149,36 @@ public void updateBDV() if ( bdv == null ) return; - for ( final ViewRegistration r : panel.getSpimData().getViewRegistrations().getViewRegistrationsOrdered() ) - r.updateModel(); + final Collection< ViewRegistration > regs = panel.getSpimData().getViewRegistrations().getViewRegistrations().values(); + regs.forEach( ViewRegistration::updateModel ); - final ViewerPanel viewerPanel = bdv.getViewer(); - final ViewerState viewerState = viewerPanel.getState(); - final List< SourceState< ? > > sources = viewerState.getSources(); - - for ( final SourceState< ? > state : sources ) - { - Source< ? > source = state.getSpimSource(); - - while ( TransformedSource.class.isInstance( source ) ) - { - source = ( ( TransformedSource< ? > ) source ).getWrappedSource(); - } + final ViewerPanel viewer = bdv.getViewer(); - if ( AbstractSpimSource.class.isInstance( source ) ) - { - final AbstractSpimSource< ? > s = ( AbstractSpimSource< ? > ) source; - - final int tpi = getCurrentTimePointIndex( s ); - callLoadTimePoint( s, tpi ); -// forceBDVReload( s ); - } + final ViewerState state = viewer.state().snapshot(); + state.getSources().forEach( BDVPopup::reloadTransformFromViewRegistrations ); + viewer.requestRepaint(); + } - if ( state.asVolatile() != null ) - { - source = state.asVolatile().getSpimSource(); - while ( TransformedSource.class.isInstance( source ) ) - { - source = ( ( TransformedSource< ? > ) source ).getWrappedSource(); - } + /** + * Calls {@link AbstractSpimSource#reload} on volatile and non-volatile + * versions nested under {@code source}. This reloads transformations from + * modified {@code ViewRegistrations}. + */ + private static void reloadTransformFromViewRegistrations( final SourceAndConverter< ? > source ) + { + Source< ? > s = source.getSpimSource(); - if ( AbstractSpimSource.class.isInstance( source ) ) - { - final AbstractSpimSource< ? > s = ( AbstractSpimSource< ? > ) source; + if ( s instanceof TransformedSource ) + s = ( ( TransformedSource ) s ).getWrappedSource(); - final int tpi = getCurrentTimePointIndex( s ); - callLoadTimePoint( s, tpi ); -// forceBDVReload( s ); - } - } - } + if ( s instanceof AbstractSpimSource ) + ( ( AbstractSpimSource< ? > ) s ).reload(); - bdv.getViewer().requestRepaint(); + if ( source.asVolatile() != null ) + reloadTransformFromViewRegistrations( source.asVolatile() ); } + @Override public boolean bdvRunning() { @@ -198,71 +186,99 @@ public boolean bdvRunning() return ( p != null && p.getBDV() != null && p.getBDV().getViewerFrame().isVisible() ); } - + public void setBDV(BigDataViewer bdv) { // close existing bdv if necessary if (bdvRunning()) new Thread(() -> {closeBDV();}).start(); - + this.bdv = bdv; ViewSetupExplorerPanel.updateBDV( this.bdv, panel.colorMode(), panel.getSpimData(), panel.firstSelectedVD(), ((GroupedRowWindow)panel).selectedRowsGroups() ); } - + /** * set BDV brightness by sampling the mid z plane (and 1/4 and 3/4 if z is large enough ) * of the currently selected source (typically the first source) and getting quantiles from intensity histogram * (slightly modified version of InitializeViewerState.initBrightness) * - * @param cumulativeMinCutoff - quantile of min - * @param cumulativeMaxCutoff - quantile of max - * @param state - Bdv's ViewerSate - * @param setupAssignments - Bdv's View assignments - * @param - type extending RealType + * @param cumulativeMinCutoff + * fraction of pixels that are allowed to be saturated at the lower end of the range. + * @param cumulativeMaxCutoff + * fraction of pixels that are allowed to be saturated at the upper end of the range. + * @param viewerFrame + * the ViewerFrame containing ViewerState and ConverterSetups */ - public static > void initBrightness( final double cumulativeMinCutoff, final double cumulativeMaxCutoff, final ViewerState state, final SetupAssignments setupAssignments ) + public static void initBrightness( final double cumulativeMinCutoff, final double cumulativeMaxCutoff, final ViewerFrame viewerFrame ) { - final Source< ? > source = state.getSources().get( state.getCurrentSource() ).getSpimSource(); - final int timepoint = state.getCurrentTimepoint(); - if ( !source.isPresent( timepoint ) ) - return; - if ( !RealType.class.isInstance( source.getType() ) ) - return; - @SuppressWarnings( "unchecked" ) - final RandomAccessibleInterval< T > img = ( RandomAccessibleInterval< T > ) source.getSource( timepoint, source.getNumMipmapLevels() - 1 ); - final long z = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 2; - - final int numBins = 6535; - final Histogram1d< T > histogram = new Histogram1d< T >( Views.iterable( Views.hyperSlice( img, 2, z ) ), new Real1dBinMapper< T >( 0, 65535, numBins, false ) ); + initBrightness( cumulativeMinCutoff, cumulativeMaxCutoff, viewerFrame.getViewerPanel().state().snapshot(), viewerFrame.getConverterSetups() ); + } - // sample some more planes if we have enough - if ( (img.max( 2 ) + 1 - img.min( 2 ) ) > 4 ) + private static void initBrightness( final double cumulativeMinCutoff, final double cumulativeMaxCutoff, final ViewerState state, final ConverterSetups converterSetups ) + { + final SourceAndConverter< ? > current = state.getCurrentSource(); + if ( current == null ) + return; + final Source< ? > source = current.getSpimSource(); + final int timepoint = state.getCurrentTimepoint(); + final Bounds bounds = estimateSourceRange( source, timepoint, cumulativeMinCutoff, cumulativeMaxCutoff ); + for ( final SourceAndConverter< ? > s : state.getSources() ) { - final long z14 = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 4; - final long z34 = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 4 * 3; - histogram.addData( Views.iterable( Views.hyperSlice( img, 2, z14 ) ) ); - histogram.addData( Views.iterable( Views.hyperSlice( img, 2, z34 ) ) ); + final ConverterSetup setup = converterSetups.getConverterSetup( s ); + setup.setDisplayRange( bounds.getMinBound(), bounds.getMaxBound() ); } + } - final DiscreteFrequencyDistribution dfd = histogram.dfd(); - final long[] bin = new long[] { 0 }; - double cumulative = 0; - int i = 0; - for ( ; i < numBins && cumulative < cumulativeMinCutoff; ++i ) - { - bin[ 0 ] = i; - cumulative += dfd.relativeFrequency( bin ); - } - final int min = i * 65535 / numBins; - for ( ; i < numBins && cumulative < cumulativeMaxCutoff; ++i ) + /** + * @param cumulativeMinCutoff + * fraction of pixels that are allowed to be saturated at the lower end of the range. + * @param cumulativeMaxCutoff + * fraction of pixels that are allowed to be saturated at the upper end of the range. + */ + private static < T extends RealType< T > > Bounds estimateSourceRange( final Source< ? > source, final int timepoint, final double cumulativeMinCutoff, final double cumulativeMaxCutoff ) + { + final Object type = source.getType(); + if ( type instanceof UnsignedShortType && source.isPresent( timepoint ) ) { - bin[ 0 ] = i; - cumulative += dfd.relativeFrequency( bin ); + final RandomAccessibleInterval< T > img = Cast.unchecked( source.getSource( timepoint, source.getNumMipmapLevels() - 1 ) ); + final double sZ0 = img.min( 2 ); + final double sZ1 = img.max( 2 ); + final long z = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 2; + + final int numBins = 6535; + final Histogram1d< T > histogram = new Histogram1d<>( Views.hyperSlice( img, 2, z ), new Real1dBinMapper<>( 0, 65535, numBins, false ) ); + + // sample some more planes if we have enough + if ( img.dimension( 2 ) > 4 ) + { + final long z14 = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 4; + final long z34 = ( img.min( 2 ) + img.max( 2 ) + 1 ) / 4 * 3; + histogram.addData( Views.hyperSlice( img, 2, z14 ) ); + histogram.addData( Views.hyperSlice( img, 2, z34 ) ); + } + + final DiscreteFrequencyDistribution dfd = histogram.dfd(); + final long[] bin = new long[] { 0 }; + double cumulative = 0; + int i = 0; + for ( ; i < numBins && cumulative < cumulativeMinCutoff; ++i ) + { + bin[ 0 ] = i; + cumulative += dfd.relativeFrequency( bin ); + } + final int min = i * 65535 / numBins; + for ( ; i < numBins && cumulative < cumulativeMaxCutoff; ++i ) + { + bin[ 0 ] = i; + cumulative += dfd.relativeFrequency( bin ); + } + final int max = i * 65535 / numBins; + return new Bounds( min, max ); } - final int max = i * 65535 / numBins; - final MinMaxGroup minmax = setupAssignments.getMinMaxGroups().get( 0 ); - minmax.getMinBoundedValue().setCurrentValue( min ); - minmax.getMaxBoundedValue().setCurrentValue( max ); + else if ( type instanceof UnsignedByteType ) + return new Bounds( 0, 255 ); + else + return new Bounds( 0, 65535 ); } public static BigDataViewer createBDV( final ExplorerWindow< ?, ? > panel ) @@ -276,7 +292,7 @@ public static BigDataViewer createBDV( final ExplorerWindow< ?, ? > panel ) return bdv; } - + public static BigDataViewer createBDV( final AbstractSpimData< ? > spimData, final String xml ) @@ -292,12 +308,9 @@ public static BigDataViewer createBDV( return null; } - BigDataViewer bdv = BigDataViewer.open( spimData, xml, IOFunctions.getProgressWriter(), ViewerOptions.options() ); - -// if ( !bdv.tryLoadSettings( panel.xml() ) ) TODO: this should work, but currently tryLoadSettings is protected. fix that. - - InitializeViewerState.initBrightness( 0.001, 0.999, bdv.getViewer(), bdv.getSetupAssignments() ); - //initBrightness( 0.001, 0.999, bdv.getViewer().getState(), bdv.getSetupAssignments() ); + final BigDataViewer bdv = BigDataViewer.open( spimData, xml, IOFunctions.getProgressWriter(), ViewerOptions.options() ); + if ( !bdv.tryLoadSettings( xml ) ) + InitializeViewerState.initBrightness( 0.001, 0.999, bdv.getViewerFrame() ); // do not rotate BDV view by default BDVPopup.initTransform( bdv.getViewer() ); @@ -338,21 +351,25 @@ public static BigDataViewer createBDV( public static void initTransform( final ViewerPanel viewer ) { - final Dimension dim = viewer.getDisplay().getSize(); - final ViewerState state = viewer.getState(); - final AffineTransform3D viewerTransform = initTransform( dim.width, dim.height, false, state ); - viewer.setCurrentViewerTransform( viewerTransform ); + final Dimension dim = viewer.getDisplayComponent().getSize(); + final AffineTransform3D viewerTransform = initTransform( dim.width, dim.height, false, viewer.state().snapshot() ); + viewer.state().setViewerTransform( viewerTransform ); } + // TODO (TP) Add initTransform without rotation to bdv-core public static AffineTransform3D initTransform( final int viewerWidth, final int viewerHeight, final boolean zoomedIn, final ViewerState state ) { - final int cX = viewerWidth / 2; - final int cY = viewerHeight / 2; + final AffineTransform3D viewerTransform = new AffineTransform3D(); + final double cX = viewerWidth / 2.0; + final double cY = viewerHeight / 2.0; - final Source< ? > source = state.getSources().get( state.getCurrentSource() ).getSpimSource(); + final SourceAndConverter< ? > current = state.getCurrentSource(); + if ( current == null ) + return viewerTransform; + final Source< ? > source = current.getSpimSource(); final int timepoint = state.getCurrentTimepoint(); if ( !source.isPresent( timepoint ) ) - return new AffineTransform3D(); + return viewerTransform; final AffineTransform3D sourceTransform = new AffineTransform3D(); source.getSourceTransform( timepoint, 0, sourceTransform ); @@ -364,9 +381,9 @@ public static AffineTransform3D initTransform( final int viewerWidth, final int final double sY1 = sourceInterval.max( 1 ); final double sZ0 = sourceInterval.min( 2 ); final double sZ1 = sourceInterval.max( 2 ); - final double sX = ( sX0 + sX1 + 1 ) / 2; - final double sY = ( sY0 + sY1 + 1 ) / 2; - final double sZ = ( sZ0 != 0 || sZ1 != 0 ) ? ( sZ0 + sZ1 + 1 ) / 2 : 0; + final double sX = ( sX0 + sX1 ) / 2; + final double sY = ( sY0 + sY1 ) / 2; + final double sZ = Math.round( ( sZ0 + sZ1 ) / 2 ); // z-slice in the middle of a pixel final double[][] m = new double[ 3 ][ 4 ]; @@ -383,7 +400,6 @@ public static AffineTransform3D initTransform( final int viewerWidth, final int LinAlgHelpers.scale( translation, -1, translation ); LinAlgHelpers.setCol( 3, translation, m ); - final AffineTransform3D viewerTransform = new AffineTransform3D(); viewerTransform.set( m ); // scale @@ -402,12 +418,11 @@ public static AffineTransform3D initTransform( final int viewerWidth, final int viewerTransform.scale( scale ); // window center offset - viewerTransform.set( viewerTransform.get( 0, 3 ) + cX, 0, 3 ); - viewerTransform.set( viewerTransform.get( 1, 3 ) + cY, 1, 3 ); + viewerTransform.set( viewerTransform.get( 0, 3 ) + cX - 0.5, 0, 3 ); + viewerTransform.set( viewerTransform.get( 1, 3 ) + cY - 0.5, 1, 3 ); return viewerTransform; } - /* This does not work yet, because invalidateAll is not implemented yet. @@ -457,76 +472,4 @@ private static final void forceBDVReload(final AbstractSpimSource< ? > s) } */ - - private static final void callLoadTimePoint( final AbstractSpimSource< ? > s, final int timePointIndex ) - { - try - { - Class< ? > clazz = null; - boolean found = false; - - do - { - if ( clazz == null ) - clazz = s.getClass(); - else - clazz = clazz.getSuperclass(); - - if ( clazz != null ) - for ( final Method method : clazz.getDeclaredMethods() ) - if ( method.getName().equals( "loadTimepoint" ) ) - found = true; - } - while ( !found && clazz != null ); - - if ( !found ) - { - System.out.println( "Failed to find SpimSource.loadTimepoint method. Quiting." ); - return; - } - - final Method loadTimepoint = clazz.getDeclaredMethod( "loadTimepoint", Integer.TYPE ); - loadTimepoint.setAccessible( true ); - loadTimepoint.invoke( s, timePointIndex ); - } - catch ( Exception e ) { e.printStackTrace(); } - } - - private static final int getCurrentTimePointIndex( final AbstractSpimSource< ? > s ) - { - try - { - Class< ? > clazz = null; - Field currentTimePointIndex = null; - - do - { - if ( clazz == null ) - clazz = s.getClass(); - else - clazz = clazz.getSuperclass(); - - if ( clazz != null ) - for ( final Field field : clazz.getDeclaredFields() ) - if ( field.getName().equals( "currentTimePointIndex" ) ) - currentTimePointIndex = field; - } - while ( currentTimePointIndex == null && clazz != null ); - - if ( currentTimePointIndex == null ) - { - System.out.println( "Failed to find AbstractSpimSource.currentTimePointIndex. Quiting." ); - return -1; - } - - currentTimePointIndex.setAccessible( true ); - - return currentTimePointIndex.getInt( s ); - } - catch ( Exception e ) - { - e.printStackTrace(); - return -1; - } - } } From 8d4a574f61a0f019c62a3f946dc37b0ce50751a5 Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Sat, 11 Nov 2023 13:52:16 +0100 Subject: [PATCH 07/13] Simplify generics --- .../mvrecon/fiji/plugin/Data_Explorer.java | 2 +- .../fiji/plugin/Interest_Point_Detection.java | 2 +- .../mvrecon/fiji/plugin/Split_Views.java | 2 +- .../spimdata/explorer/ExplorerWindow.java | 6 ++-- .../explorer/FilteredAndGroupedExplorer.java | 7 ++-- .../FilteredAndGroupedExplorerPanel.java | 36 +++++++++---------- .../FilteredAndGroupedTableModel.java | 8 ++--- .../spimdata/explorer/GroupedRowWindow.java | 2 +- .../explorer/ISpimDataTableModel.java | 8 ++--- .../MissingViewsTableModelDecorator.java | 2 +- .../MultiViewTableModelDecorator.java | 2 +- .../SelectedViewDescriptionListener.java | 2 +- .../spimdata/explorer/ViewSetupExplorer.java | 6 ++-- .../explorer/ViewSetupExplorerPanel.java | 4 +-- .../interestpoint/InterestPointExplorer.java | 6 ++-- .../InterestPointExplorerPanel.java | 4 +-- .../popup/ApplyTransformationPopup.java | 8 ++--- .../spimdata/explorer/popup/BDVPopup.java | 6 ++-- .../popup/BakeManualTransformationPopup.java | 4 +-- .../explorer/popup/BoundingBoxPopup.java | 4 +-- .../explorer/popup/DeconvolutionPopup.java | 4 +-- .../popup/DetectInterestPointsPopup.java | 4 +-- .../popup/DisplayFusedImagesPopup.java | 4 +-- .../explorer/popup/DisplayRawImagesPopup.java | 4 +-- .../explorer/popup/ExplorerWindowSetable.java | 2 +- .../popup/FlatFieldCorrectionPopup.java | 4 +-- .../spimdata/explorer/popup/FusionPopup.java | 4 +-- .../popup/IntensityAdjustmentPopup.java | 4 +-- .../popup/InterestPointsExplorerPopup.java | 12 +++---- .../spimdata/explorer/popup/LabelPopUp.java | 2 +- .../explorer/popup/MaxProjectPopup.java | 4 +-- .../popup/PointSpreadFunctionsPopup.java | 4 +-- .../spimdata/explorer/popup/QualityPopup.java | 4 +-- .../popup/RegisterInterestPointsPopup.java | 4 +-- .../popup/RegistrationExplorerPopup.java | 12 +++---- .../explorer/popup/RemoveDetectionsPopup.java | 4 +-- .../popup/RemoveTransformationPopup.java | 4 +-- .../explorer/popup/ReorientSamplePopup.java | 4 +-- .../spimdata/explorer/popup/ResavePopup.java | 6 ++-- .../spimdata/explorer/popup/Separator.java | 2 +- .../explorer/popup/SimpleHyperlinkPopup.java | 2 +- .../popup/SpecifyCalibrationPopup.java | 4 +-- .../popup/VisualizeDetectionsPopup.java | 4 +-- .../explorer/popup/VisualizeNonRigid.java | 4 +-- .../registration/RegistrationExplorer.java | 8 ++--- .../RegistrationExplorerPanel.java | 10 +++--- .../headless/splitting/TestSplitting.java | 2 +- 47 files changed, 123 insertions(+), 124 deletions(-) diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/Data_Explorer.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/Data_Explorer.java index 87a45c5dc..6b08e0068 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/plugin/Data_Explorer.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/plugin/Data_Explorer.java @@ -73,7 +73,7 @@ public void actionPerformed(ActionEvent e) final String xml = result.getXMLFileName(); final XmlIoSpimData2 io = result.getIO(); - final ViewSetupExplorer< SpimData2, XmlIoSpimData2 > explorer = new ViewSetupExplorer( data, xml, io ); + final ViewSetupExplorer< SpimData2 > explorer = new ViewSetupExplorer<>( data, xml, io ); explorer.getFrame().toFront(); } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/Interest_Point_Detection.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/Interest_Point_Detection.java index 55278a5d7..ec0736cbd 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/plugin/Interest_Point_Detection.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/plugin/Interest_Point_Detection.java @@ -66,7 +66,7 @@ public class Interest_Point_Detection implements PlugIn public static boolean defaultGroupTiles = true; public static boolean defaultGroupIllums = true; - public static ExplorerWindow< ?, ? > currentPanel; + public static ExplorerWindow< ? > currentPanel; static { diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/Split_Views.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/Split_Views.java index 6003a8292..5e2bc5a85 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/plugin/Split_Views.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/plugin/Split_Views.java @@ -86,7 +86,7 @@ public static boolean split( if ( display ) { - final ViewSetupExplorer< SpimData2, XmlIoSpimData2 > explorer = new ViewSetupExplorer( newSD, saveAs, new XmlIoSpimData2( "" ) ); + final ViewSetupExplorer< SpimData2 > explorer = new ViewSetupExplorer<>( newSD, saveAs, new XmlIoSpimData2( "" ) ); explorer.getFrame().toFront(); } else diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ExplorerWindow.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ExplorerWindow.java index 10a754b76..26435afca 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ExplorerWindow.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ExplorerWindow.java @@ -32,9 +32,9 @@ import mpicbg.spim.data.generic.sequence.BasicViewSetup; import mpicbg.spim.data.sequence.ViewId; -public interface ExplorerWindow< AS extends AbstractSpimData< ? >, X extends XmlIoAbstractSpimData< ?, AS > > +public interface ExplorerWindow< AS extends AbstractSpimData< ? > > { - public List< BasicViewDescription< ? extends BasicViewSetup > > selectedRows(); + public List< BasicViewDescription< ? > > selectedRows(); public List< ViewId > selectedRowsViewId(); public AS getSpimData(); public void updateContent(); @@ -48,5 +48,5 @@ public interface ExplorerWindow< AS extends AbstractSpimData< ? >, X extends Xml // BDV-specific public BasicBDVPopup bdvPopup(); public boolean colorMode(); - public BasicViewDescription< ? extends BasicViewSetup > firstSelectedVD(); + public BasicViewDescription< ? > firstSelectedVD(); } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorer.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorer.java index 7998a264b..5e0642f8c 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorer.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorer.java @@ -27,19 +27,18 @@ import javax.swing.JFrame; import mpicbg.spim.data.generic.AbstractSpimData; -import mpicbg.spim.data.generic.XmlIoAbstractSpimData; -public abstract class FilteredAndGroupedExplorer, X extends XmlIoAbstractSpimData< ?, AS >> +public abstract class FilteredAndGroupedExplorer > { protected JFrame frame; - protected FilteredAndGroupedExplorerPanel< AS, X > panel; + protected FilteredAndGroupedExplorerPanel< AS > panel; public AS getSpimData() { return panel.getSpimData(); } - public FilteredAndGroupedExplorerPanel< AS, X > getPanel() + public FilteredAndGroupedExplorerPanel< AS > getPanel() { return panel; } public JFrame getFrame() diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java index a84abdb8b..2e74f3ffa 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java @@ -69,10 +69,10 @@ import net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPoints; import net.preibisch.mvrecon.process.interestpointregistration.TransformationTools; -public abstract class FilteredAndGroupedExplorerPanel, X extends XmlIoAbstractSpimData< ?, AS >> - extends JPanel implements ExplorerWindow< AS, X >, GroupedRowWindow +public abstract class FilteredAndGroupedExplorerPanel > + extends JPanel implements ExplorerWindow< AS >, GroupedRowWindow { - public static FilteredAndGroupedExplorerPanel< ?, ? > currentInstance = null; + public static FilteredAndGroupedExplorerPanel< ? > currentInstance = null; protected ArrayList< ExplorerWindowSetable > popups; @@ -89,18 +89,17 @@ public abstract class FilteredAndGroupedExplorerPanel tableModel; protected ArrayList< SelectedViewDescriptionListener< AS > > listeners; protected AS data; - protected FilteredAndGroupedExplorer< AS, X > explorer; + protected FilteredAndGroupedExplorer< AS > explorer; protected final String xml; - protected final X io; + protected final XmlIoAbstractSpimData< ?, AS > io; protected final boolean isMac; protected boolean colorMode = false; - - final protected HashSet< List> > selectedRows; + final protected HashSet< List< BasicViewDescription< ? > > > selectedRows; protected BasicViewDescription< ? extends BasicViewSetup > firstSelectedVD; - public FilteredAndGroupedExplorerPanel(final FilteredAndGroupedExplorer< AS, X > explorer, final AS data, - final String xml, final X io) + public FilteredAndGroupedExplorerPanel(final FilteredAndGroupedExplorer< AS > explorer, final AS data, + final String xml, final XmlIoAbstractSpimData< ?, AS > io) { @@ -165,12 +164,12 @@ public String xml() return xml; } - public X io() + public XmlIoAbstractSpimData< ?, AS > io() { return io; } - public FilteredAndGroupedExplorer< AS, X > explorer() + public FilteredAndGroupedExplorer< AS > explorer() { return explorer; } @@ -220,8 +219,8 @@ public void addListener(final SelectedViewDescriptionListener< AS > listener) { this.listeners.add( listener ); - List>> selectedList = new ArrayList<>(); - for (List> selectedI : selectedRows) + List>> selectedList = new ArrayList<>(); + for (List> selectedI : selectedRows) selectedList.add( selectedI ); listener.selectedViewDescriptions( selectedList ); @@ -238,7 +237,7 @@ public void updateFilter(Class entityClass, Entity selectedIns { ArrayList selectedInstances = new ArrayList<>(); selectedInstances.add( selectedInstance ); - tableModel.addFilter( entityClass, selectedInstances ); + tableModel.addFilter( entityClass, selectedInstances ); } protected static List getEntityNamesOrIds(List entities) @@ -300,8 +299,9 @@ public void valueChanged(final ListSelectionEvent arg0) selectedRows.add( tableModel.getElements().get( row ) ); } - List>> selectedList = new ArrayList<>(); - for (List> selectedI : selectedRows) + + List>> selectedList = new ArrayList<>(); + for (List> selectedI : selectedRows) selectedList.add( selectedI ); for ( int i = 0; i < listeners.size(); ++i ) @@ -385,7 +385,7 @@ public static void resetBDVManualTransformations(BigDataViewer bdv) public static void updateBDV(final BigDataViewer bdv, final boolean colorMode, final AbstractSpimData< ? > data, BasicViewDescription< ? extends BasicViewSetup > firstVD, - final Collection< List< BasicViewDescription< ? extends BasicViewSetup >> > selectedRows) + final Collection< List< BasicViewDescription< ? > > > selectedRows ) { // bdv is not open @@ -720,7 +720,7 @@ public void keyTyped(final KeyEvent arg0){} public abstract ArrayList< ExplorerWindowSetable > initPopups(); @Override - public Collection< List< BasicViewDescription< ? extends BasicViewSetup > > > selectedRowsGroups() + public Collection< List< BasicViewDescription< ? > > > selectedRowsGroups() { return selectedRows; } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedTableModel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedTableModel.java index 7177c5ce8..c6a7dce09 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedTableModel.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedTableModel.java @@ -57,8 +57,8 @@ public class FilteredAndGroupedTableModel < AS extends AbstractSpimData< ? > > e private static final long serialVersionUID = -6526338840427674269L; protected List< List< BasicViewDescription< ? > >> elements = null; - - final ExplorerWindow< AS, ? > panel; + + final ExplorerWindow< AS > panel; Set> groupingFactors; Map, List> filters; List> columnClasses; @@ -68,7 +68,7 @@ public class FilteredAndGroupedTableModel < AS extends AbstractSpimData< ? > > e * @see gui.ISpimDataTableModel#getPanel() */ @Override - public ExplorerWindow< AS, ? > getPanel() { + public ExplorerWindow< AS > getPanel() { return panel; } @@ -155,7 +155,7 @@ public static ArrayList> defaultColumnClassesMV() return res; } - public FilteredAndGroupedTableModel( final ExplorerWindow< AS, ? > panel ) + public FilteredAndGroupedTableModel( final ExplorerWindow< AS > panel ) { groupingFactors = new HashSet<>(); filters = new HashMap<>(); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/GroupedRowWindow.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/GroupedRowWindow.java index 7f9de18d5..d1350f158 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/GroupedRowWindow.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/GroupedRowWindow.java @@ -31,6 +31,6 @@ public interface GroupedRowWindow { - public Collection >> selectedRowsGroups(); + public Collection< List< BasicViewDescription< ? > > > selectedRowsGroups(); public List> selectedRowsViewIdGroups(); } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ISpimDataTableModel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ISpimDataTableModel.java index 205bae6c5..1961958b1 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ISpimDataTableModel.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ISpimDataTableModel.java @@ -42,9 +42,9 @@ public enum SpecialColumnType{ } public int getSpecialColumn(SpecialColumnType type); - - public ExplorerWindow< AS, ? > getPanel(); - + + public ExplorerWindow< AS > getPanel(); + public Set> getGroupingFactors(); public void clearSortingFactors(); @@ -61,7 +61,7 @@ public enum SpecialColumnType{ public Map , List> getFilters(); - public List> > getElements(); + public List< List< BasicViewDescription< ? > > > getElements(); public void updateElements(); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MissingViewsTableModelDecorator.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MissingViewsTableModelDecorator.java index 98584a621..e5a00ab81 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MissingViewsTableModelDecorator.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MissingViewsTableModelDecorator.java @@ -117,7 +117,7 @@ public int getSpecialColumn(net.preibisch.mvrecon.fiji.spimdata.explorer.ISpimDa } @Override - public ExplorerWindow< AS, ? > getPanel() + public ExplorerWindow< AS > getPanel() { return decorated.getPanel(); } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MultiViewTableModelDecorator.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MultiViewTableModelDecorator.java index 4ff169e3c..f24cf1d92 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MultiViewTableModelDecorator.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MultiViewTableModelDecorator.java @@ -244,7 +244,7 @@ public void sortByColumn(int column) { } @Override - public ExplorerWindow getPanel() { return decorated.getPanel(); } + public ExplorerWindow getPanel() { return decorated.getPanel(); } @Override public void setValueAt(Object aValue, int rowIndex, int columnIndex) diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/SelectedViewDescriptionListener.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/SelectedViewDescriptionListener.java index f26043b5b..fffd00801 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/SelectedViewDescriptionListener.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/SelectedViewDescriptionListener.java @@ -30,7 +30,7 @@ public interface SelectedViewDescriptionListener< AS extends AbstractSpimData< ? > > { //public void firstSelectedViewDescriptions( List< BasicViewDescription< ? extends BasicViewSetup > > viewDescriptions ); - public void selectedViewDescriptions( List< List< BasicViewDescription< ? extends BasicViewSetup > > > viewDescriptions ); + public void selectedViewDescriptions( List< List< BasicViewDescription< ? > > > viewDescriptions ); public void updateContent( final AS data ); public void save(); public void quit(); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorer.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorer.java index b47734a56..8369fe8c7 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorer.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorer.java @@ -34,17 +34,17 @@ import mpicbg.spim.data.generic.AbstractSpimData; import mpicbg.spim.data.generic.XmlIoAbstractSpimData; -public class ViewSetupExplorer< AS extends AbstractSpimData< ? >, X extends XmlIoAbstractSpimData< ?, AS > > extends FilteredAndGroupedExplorer< AS, X > +public class ViewSetupExplorer< AS extends AbstractSpimData< ? > > extends FilteredAndGroupedExplorer< AS > { public static final double xPos = 0.4; public static final double yPos = 0.4; public static final double xPosLog = 0.0; public static final double yPosLog = 0.8; - public ViewSetupExplorer( final AS data, final String xml, final X io ) + public ViewSetupExplorer( final AS data, final String xml, final XmlIoAbstractSpimData< ?, AS > io ) { frame = new JFrame( "ViewSetup Explorer" ); - panel = new ViewSetupExplorerPanel< AS, X >( this, data, xml, io, true ); + panel = new ViewSetupExplorerPanel< AS >( this, data, xml, io, true ); frame.add( panel, BorderLayout.CENTER ); frame.setSize( panel.getPreferredSize() ); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorerPanel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorerPanel.java index c6c3d6714..5a90e4a15 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorerPanel.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorerPanel.java @@ -111,7 +111,7 @@ import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group; -public class ViewSetupExplorerPanel< AS extends AbstractSpimData< ? >, X extends XmlIoAbstractSpimData< ?, AS > > extends FilteredAndGroupedExplorerPanel< AS, X > implements ExplorerWindow< AS, X > +public class ViewSetupExplorerPanel< AS extends AbstractSpimData< ? > > extends FilteredAndGroupedExplorerPanel< AS > implements ExplorerWindow< AS > { private static final long serialVersionUID = -2512096359830259015L; @@ -145,7 +145,7 @@ public boolean illumsGrouped() @Override public boolean channelsGrouped() { return false; } - public ViewSetupExplorerPanel( final FilteredAndGroupedExplorer< AS, X > explorer, final AS data, final String xml, final X io, boolean requestStartBDV ) + public ViewSetupExplorerPanel( final FilteredAndGroupedExplorer< AS > explorer, final AS data, final String xml, final XmlIoAbstractSpimData< ?, AS > io, boolean requestStartBDV ) { super( explorer, data, xml, io ); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorer.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorer.java index ad903fc2f..d9fede760 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorer.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorer.java @@ -46,15 +46,15 @@ import net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BasicBDVPopup; import net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints; -public class InterestPointExplorer< AS extends SpimData2, X extends XmlIoAbstractSpimData< ?, AS > > +public class InterestPointExplorer< AS extends SpimData2 > implements SelectedViewDescriptionListener< AS > { final String xml; final JFrame frame; final InterestPointExplorerPanel panel; - final FilteredAndGroupedExplorer< AS, X > viewSetupExplorer; + final FilteredAndGroupedExplorer< AS > viewSetupExplorer; - public InterestPointExplorer( final String xml, final X io, final FilteredAndGroupedExplorer< AS, X > viewSetupExplorer ) + public InterestPointExplorer( final String xml, final XmlIoAbstractSpimData< ?, AS > io, final FilteredAndGroupedExplorer< AS > viewSetupExplorer ) { this.xml = xml; this.viewSetupExplorer = viewSetupExplorer; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorerPanel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorerPanel.java index 5f2252953..ba140f75c 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorerPanel.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorerPanel.java @@ -63,7 +63,7 @@ public class InterestPointExplorerPanel extends JPanel { private static final long serialVersionUID = -3767947754096099774L; - final FilteredAndGroupedExplorer< ?, ? > viewSetupExplorer; + final FilteredAndGroupedExplorer< ? > viewSetupExplorer; protected JTable table; protected InterestPointTableModel tableModel; @@ -73,7 +73,7 @@ public class InterestPointExplorerPanel extends JPanel //protected ArrayList< Pair< InterestPointList, ViewId > > save; protected ArrayList< Pair< InterestPoints, ViewId > > delete; - public InterestPointExplorerPanel( final ViewInterestPoints viewInterestPoints, final FilteredAndGroupedExplorer< ?, ? > viewSetupExplorer ) + public InterestPointExplorerPanel( final ViewInterestPoints viewInterestPoints, final FilteredAndGroupedExplorer< ? > viewSetupExplorer ) { //this.save = new ArrayList< Pair< InterestPointList, ViewId > >(); this.delete = new ArrayList< Pair< InterestPoints, ViewId > >(); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ApplyTransformationPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ApplyTransformationPopup.java index 274a2c97f..b11037837 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ApplyTransformationPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ApplyTransformationPopup.java @@ -47,7 +47,7 @@ public class ApplyTransformationPopup extends JMenuItem implements ExplorerWindo private static final long serialVersionUID = 5234649267634013390L; public static boolean showWarning = true; - ExplorerWindow< ?, ? > panel; + ExplorerWindow< ? > panel; public ApplyTransformationPopup() { @@ -57,19 +57,19 @@ public ApplyTransformationPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; return this; } - public static final List< ViewId > getSelectedViews( final ExplorerWindow< ?, ? > panel ) + public static final List< ViewId > getSelectedViews( final ExplorerWindow< ? > panel ) { return getSelectedViews( panel, true ); } public static final List< ViewId > getSelectedViews( - final ExplorerWindow< ?, ? > panel, + final ExplorerWindow< ? > panel, final boolean filterMissing ) { final List< ViewId > viewIds = new ArrayList<>(); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java index 8f7d01d7f..5ecdffa8f 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java @@ -70,7 +70,7 @@ public class BDVPopup extends JMenuItem implements ExplorerWindowSetable, BasicB { private static final long serialVersionUID = 5234649267634013390L; - public ExplorerWindow< ?, ? > panel; + public ExplorerWindow< ? > panel; public BigDataViewer bdv = null; public BDVPopup() @@ -81,7 +81,7 @@ public BDVPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; return this; @@ -281,7 +281,7 @@ else if ( type instanceof UnsignedByteType ) return new Bounds( 0, 65535 ); } - public static BigDataViewer createBDV( final ExplorerWindow< ?, ? > panel ) + public static BigDataViewer createBDV( final ExplorerWindow< ? > panel ) { final BigDataViewer bdv = createBDV( panel.getSpimData(), panel.xml() ); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BakeManualTransformationPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BakeManualTransformationPopup.java index 95eb9e57c..24cbdef7a 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BakeManualTransformationPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BakeManualTransformationPopup.java @@ -46,7 +46,7 @@ public class BakeManualTransformationPopup extends JMenuItem implements Explorer { private static final long serialVersionUID = 4627408819269954486L; - ExplorerWindow< ?, ? > panel; + ExplorerWindow< ? > panel; public BakeManualTransformationPopup() { @@ -56,7 +56,7 @@ public BakeManualTransformationPopup() } @Override - public JComponent setExplorerWindow( ExplorerWindow< ?, ? > panel ) + public JComponent setExplorerWindow( ExplorerWindow< ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BoundingBoxPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BoundingBoxPopup.java index 531194425..41e0f1cae 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BoundingBoxPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BoundingBoxPopup.java @@ -42,7 +42,7 @@ public class BoundingBoxPopup extends JMenuItem implements ExplorerWindowSetable { private static final long serialVersionUID = 5234649267634013390L; - ExplorerWindow< ?, ? > panel; + ExplorerWindow< ? > panel; public BoundingBoxPopup() { @@ -52,7 +52,7 @@ public BoundingBoxPopup() } @Override - public JComponent setExplorerWindow( ExplorerWindow>, ?> panel ) + public JComponent setExplorerWindow( ExplorerWindow< ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DeconvolutionPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DeconvolutionPopup.java index b60c50d30..f29674463 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DeconvolutionPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DeconvolutionPopup.java @@ -39,7 +39,7 @@ public class DeconvolutionPopup extends JMenuItem implements ExplorerWindowSetab { private static final long serialVersionUID = 5234649267634013390L; - ExplorerWindow< ?, ? > panel; + ExplorerWindow< ? > panel; public DeconvolutionPopup() { @@ -49,7 +49,7 @@ public DeconvolutionPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DetectInterestPointsPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DetectInterestPointsPopup.java index 327fca94a..e4c51cc3b 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DetectInterestPointsPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DetectInterestPointsPopup.java @@ -39,7 +39,7 @@ public class DetectInterestPointsPopup extends JMenuItem implements ExplorerWind { private static final long serialVersionUID = 5234649267634013390L; - ExplorerWindow< ?, ? > panel; + ExplorerWindow< ? > panel; public DetectInterestPointsPopup() { @@ -49,7 +49,7 @@ public DetectInterestPointsPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayFusedImagesPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayFusedImagesPopup.java index 527963979..2e46f2bea 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayFusedImagesPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayFusedImagesPopup.java @@ -71,7 +71,7 @@ public class DisplayFusedImagesPopup extends JMenu implements ExplorerWindowSeta private static final long serialVersionUID = -4895470813542722644L; - ExplorerWindow< ?, ? > panel = null; + ExplorerWindow< ? > panel = null; public DisplayFusedImagesPopup() { @@ -162,7 +162,7 @@ public void menuCanceled( MenuEvent e ) {} } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayRawImagesPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayRawImagesPopup.java index 27c01c300..23b121125 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayRawImagesPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/DisplayRawImagesPopup.java @@ -42,7 +42,7 @@ public class DisplayRawImagesPopup extends JMenu implements ExplorerWindowSetabl public static final int askWhenMoreThan = 5; private static final long serialVersionUID = 5234649262342301390L; - ExplorerWindow< ?, ? > panel = null; + ExplorerWindow< ? > panel = null; public DisplayRawImagesPopup() { @@ -59,7 +59,7 @@ public DisplayRawImagesPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ExplorerWindowSetable.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ExplorerWindowSetable.java index 52e0e079c..dc633deca 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ExplorerWindowSetable.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ExplorerWindowSetable.java @@ -31,6 +31,6 @@ public interface ExplorerWindowSetable { - public JComponent setExplorerWindow( final ExplorerWindow< ?, ? > panel ); + public JComponent setExplorerWindow( final ExplorerWindow< ? > panel ); } // AbstractSpimData< ? extends AbstractSequenceDescription< ?, ?, ? > > diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FlatFieldCorrectionPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FlatFieldCorrectionPopup.java index 37a4bcbe0..d169de4e4 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FlatFieldCorrectionPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FlatFieldCorrectionPopup.java @@ -52,7 +52,7 @@ public class FlatFieldCorrectionPopup extends JMenuItem implements ExplorerWindo { private static final long serialVersionUID = 950277697000203629L; - private ExplorerWindow< ?, ? > panel; + private ExplorerWindow< ? > panel; public FlatFieldCorrectionPopup() { @@ -61,7 +61,7 @@ public FlatFieldCorrectionPopup() } @Override - public JComponent setExplorerWindow( ExplorerWindow< ?, ? > panel ) + public JComponent setExplorerWindow( ExplorerWindow< ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FusionPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FusionPopup.java index 55c008f47..020170cca 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FusionPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/FusionPopup.java @@ -39,7 +39,7 @@ public class FusionPopup extends JMenuItem implements ExplorerWindowSetable { private static final long serialVersionUID = 5234649267634013390L; - ExplorerWindow< ?, ? > panel; + ExplorerWindow< ? > panel; public FusionPopup() { @@ -49,7 +49,7 @@ public FusionPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/IntensityAdjustmentPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/IntensityAdjustmentPopup.java index 96d9b6a6f..924919307 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/IntensityAdjustmentPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/IntensityAdjustmentPopup.java @@ -43,7 +43,7 @@ public class IntensityAdjustmentPopup extends JMenu implements ExplorerWindowSet { private static final long serialVersionUID = 1L; - ExplorerWindow< ?, ? > panel; + ExplorerWindow< ? > panel; protected static String[] types = new String[]{ "Compute ...", "List all", "Remove" }; @@ -65,7 +65,7 @@ public IntensityAdjustmentPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/InterestPointsExplorerPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/InterestPointsExplorerPopup.java index 76ca00198..054b40992 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/InterestPointsExplorerPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/InterestPointsExplorerPopup.java @@ -40,8 +40,8 @@ public class InterestPointsExplorerPopup extends JMenuItem implements ExplorerWi { private static final long serialVersionUID = 5234649267634013390L; - ViewSetupExplorerPanel< ?, ? > panel; - InterestPointExplorer< ?, ? > ipe = null; + ViewSetupExplorerPanel< ? > panel; + InterestPointExplorer< ? > ipe = null; public InterestPointsExplorerPopup() { @@ -52,9 +52,9 @@ public InterestPointsExplorerPopup() @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { - this.panel = (ViewSetupExplorerPanel< ?, ? >)panel; + this.panel = (ViewSetupExplorerPanel< ? >)panel; return this; } @@ -94,8 +94,8 @@ public void run() } } - private static final < AS extends SpimData2, X extends XmlIoAbstractSpimData< ?, AS > > InterestPointExplorer< AS, X > instanceFor( final FilteredAndGroupedExplorerPanel< AS, X > panel ) + private static < AS extends SpimData2 > InterestPointExplorer< AS > instanceFor( final FilteredAndGroupedExplorerPanel< AS > panel ) { - return new InterestPointExplorer< AS, X >( panel.xml(), panel.io(), panel.explorer() ); + return new InterestPointExplorer<>( panel.xml(), panel.io(), panel.explorer() ); } } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/LabelPopUp.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/LabelPopUp.java index 8fc502a8b..90cb8ac6d 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/LabelPopUp.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/LabelPopUp.java @@ -41,7 +41,7 @@ public LabelPopUp( final String text ) } @Override - public JLabel setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JLabel setExplorerWindow( final ExplorerWindow< ? > panel ) { return this; } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/MaxProjectPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/MaxProjectPopup.java index b71bc6533..fe3572aca 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/MaxProjectPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/MaxProjectPopup.java @@ -44,7 +44,7 @@ public class MaxProjectPopup extends JMenuItem implements ExplorerWindowSetable private static final long serialVersionUID = 5234649267634013390L; public static boolean showWarning = true; - ExplorerWindow< ?, ? > panel; + ExplorerWindow< ? > panel; public MaxProjectPopup() { @@ -54,7 +54,7 @@ public MaxProjectPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/PointSpreadFunctionsPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/PointSpreadFunctionsPopup.java index f97763264..e90f1514a 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/PointSpreadFunctionsPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/PointSpreadFunctionsPopup.java @@ -50,10 +50,10 @@ public class PointSpreadFunctionsPopup extends JMenu implements ExplorerWindowSe { private static final long serialVersionUID = 1L; - ExplorerWindow< ?, ? > panel = null; + ExplorerWindow< ? > panel = null; @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/QualityPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/QualityPopup.java index 8dae96d7c..b0d28224d 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/QualityPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/QualityPopup.java @@ -40,7 +40,7 @@ public class QualityPopup extends JMenuItem implements ExplorerWindowSetable { private static final long serialVersionUID = 5234649267634013390L; - ExplorerWindow< ?, ? > panel; + ExplorerWindow< ? > panel; public QualityPopup() { @@ -50,7 +50,7 @@ public QualityPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegisterInterestPointsPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegisterInterestPointsPopup.java index 243dcbdf1..e255a36a7 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegisterInterestPointsPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegisterInterestPointsPopup.java @@ -39,7 +39,7 @@ public class RegisterInterestPointsPopup extends JMenuItem implements ExplorerWi { private static final long serialVersionUID = 5234649267634013390L; - ExplorerWindow< ?, ? > panel; + ExplorerWindow< ? > panel; public RegisterInterestPointsPopup() { @@ -49,7 +49,7 @@ public RegisterInterestPointsPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegistrationExplorerPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegistrationExplorerPopup.java index d6b4cfa1e..8002c2279 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegistrationExplorerPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RegistrationExplorerPopup.java @@ -41,8 +41,8 @@ public class RegistrationExplorerPopup extends JMenuItem implements ExplorerWind { private static final long serialVersionUID = 5234649267634013390L; - FilteredAndGroupedExplorerPanel< ?, ? > panel; - RegistrationExplorer< ?, ? > re = null; + FilteredAndGroupedExplorerPanel< ? > panel; + RegistrationExplorer< ? > re = null; public RegistrationExplorerPopup() { @@ -52,9 +52,9 @@ public RegistrationExplorerPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { - this.panel = (FilteredAndGroupedExplorerPanel< ?, ? >)panel; + this.panel = ( FilteredAndGroupedExplorerPanel< ? > ) panel; return this; } @@ -88,8 +88,8 @@ public void run() } } - private static final < AS extends AbstractSpimData< ? >, X extends XmlIoAbstractSpimData< ?, AS > > RegistrationExplorer< AS, X > instanceFor( final FilteredAndGroupedExplorerPanel< AS, X > panel ) + private static < AS extends AbstractSpimData< ? > > RegistrationExplorer< AS > instanceFor( final FilteredAndGroupedExplorerPanel< AS > panel ) { - return new RegistrationExplorer< AS, X >( panel.xml(), panel.io(), panel.explorer() ); + return new RegistrationExplorer<>( panel.xml(), panel.io(), panel.explorer() ); } } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveDetectionsPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveDetectionsPopup.java index 4417c075f..9db5f6b16 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveDetectionsPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveDetectionsPopup.java @@ -57,7 +57,7 @@ public class RemoveDetectionsPopup extends JMenu implements ExplorerWindowSetabl { private static final long serialVersionUID = 1L; - ExplorerWindow< ?, ? > panel = null; + ExplorerWindow< ? > panel = null; public static int defaultLabel = 0; public static String defaultNewLabel = "Manually removed"; @@ -141,7 +141,7 @@ public void menuCanceled( MenuEvent e ) {} } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveTransformationPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveTransformationPopup.java index 1907f54ab..4eabbe4c0 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveTransformationPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/RemoveTransformationPopup.java @@ -42,7 +42,7 @@ public class RemoveTransformationPopup extends JMenu implements ExplorerWindowSe public static final int askWhenMoreThan = 5; private static final long serialVersionUID = 5234649267634013390L; - ExplorerWindow< ?, ? > panel; + ExplorerWindow< ? > panel; protected static String[] types = new String[]{ "Latest/Newest Transformation", "First/Oldest Transformation" }; @@ -61,7 +61,7 @@ public RemoveTransformationPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ReorientSamplePopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ReorientSamplePopup.java index 0b6b359c9..df981c131 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ReorientSamplePopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ReorientSamplePopup.java @@ -46,7 +46,7 @@ public class ReorientSamplePopup extends JMenuItem implements ExplorerWindowSeta private static final long serialVersionUID = 5234649267634013390L; public static boolean showWarning = true; - ExplorerWindow< ?, ? > panel; + ExplorerWindow< ? > panel; public ReorientSamplePopup() { @@ -56,7 +56,7 @@ public ReorientSamplePopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java index 7c2492332..05d98dd08 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java @@ -58,7 +58,7 @@ public class ResavePopup extends JMenu implements ExplorerWindowSetable public static final int askWhenMoreThan = 5; private static final long serialVersionUID = 5234649267634013390L; - FilteredAndGroupedExplorerPanel< ?, ? > panel; + FilteredAndGroupedExplorerPanel< ? > panel; protected static String[] types = new String[]{ "As TIFF ...", "As compressed TIFF ...", "As HDF5 ...", "As compressed HDF5 ...", "As compressed N5 ..." }; @@ -86,9 +86,9 @@ public ResavePopup() } @Override - public JMenuItem setExplorerWindow( ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( ExplorerWindow< ? > panel ) { - this.panel = ( FilteredAndGroupedExplorerPanel< ?, ? > ) panel; + this.panel = ( FilteredAndGroupedExplorerPanel< ? > ) panel; return this; } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/Separator.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/Separator.java index c6049aca3..2db7e1615 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/Separator.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/Separator.java @@ -31,7 +31,7 @@ public class Separator extends JSeparator implements ExplorerWindowSetable private static final long serialVersionUID = 5234649267634013390L; @Override - public JSeparator setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JSeparator setExplorerWindow( final ExplorerWindow< ? > panel ) { return this; } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SimpleHyperlinkPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SimpleHyperlinkPopup.java index fda8bf482..78d3a2412 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SimpleHyperlinkPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SimpleHyperlinkPopup.java @@ -52,7 +52,7 @@ public SimpleHyperlinkPopup(String title, URI uri) } @Override - public JComponent setExplorerWindow( ExplorerWindow< ?, ? > panel ) + public JComponent setExplorerWindow( ExplorerWindow< ? > panel ) { return this; } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SpecifyCalibrationPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SpecifyCalibrationPopup.java index 99e0fcc9e..d3d0c1f22 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SpecifyCalibrationPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/SpecifyCalibrationPopup.java @@ -45,7 +45,7 @@ public class SpecifyCalibrationPopup extends JMenuItem implements ExplorerWindow private static final long serialVersionUID = 5234649267634013390L; public static boolean showWarning = true; - ExplorerWindow< ?, ? > panel; + ExplorerWindow< ? > panel; public SpecifyCalibrationPopup() { @@ -55,7 +55,7 @@ public SpecifyCalibrationPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeDetectionsPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeDetectionsPopup.java index b0bc4b432..3e9c905e9 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeDetectionsPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeDetectionsPopup.java @@ -40,7 +40,7 @@ public class VisualizeDetectionsPopup extends JMenuItem implements ExplorerWindo { private static final long serialVersionUID = 5234649267634013390L; - ExplorerWindow< ?, ? > panel; + ExplorerWindow< ? > panel; public VisualizeDetectionsPopup() { @@ -50,7 +50,7 @@ public VisualizeDetectionsPopup() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeNonRigid.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeNonRigid.java index 647517153..9e40e8828 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeNonRigid.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/VisualizeNonRigid.java @@ -69,7 +69,7 @@ public class VisualizeNonRigid extends JMenuItem implements ExplorerWindowSetabl { private static final long serialVersionUID = -4858927229313796971L; - ExplorerWindow< ?, ? > panel; + ExplorerWindow< ? > panel; final private static String[] displayOptions = new String[] { "Overlay all views affine vs. non-rigid", @@ -87,7 +87,7 @@ public VisualizeNonRigid() } @Override - public JMenuItem setExplorerWindow( final ExplorerWindow< ?, ? > panel ) + public JMenuItem setExplorerWindow( final ExplorerWindow< ? > panel ) { this.panel = panel; return this; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorer.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorer.java index 18eaa839c..d5a531754 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorer.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorer.java @@ -40,15 +40,15 @@ import mpicbg.spim.data.generic.sequence.BasicViewDescription; import mpicbg.spim.data.generic.sequence.BasicViewSetup; -public class RegistrationExplorer< AS extends AbstractSpimData< ? >, X extends XmlIoAbstractSpimData< ?, AS > > +public class RegistrationExplorer< AS extends AbstractSpimData< ? > > implements SelectedViewDescriptionListener< AS > { final String xml; final JFrame frame; final RegistrationExplorerPanel panel; - final FilteredAndGroupedExplorer< AS, X > viewSetupExplorer; - - public RegistrationExplorer( final String xml, final X io, final FilteredAndGroupedExplorer< AS, X > viewSetupExplorer ) + final FilteredAndGroupedExplorer< AS > viewSetupExplorer; + + public RegistrationExplorer( final String xml, final XmlIoAbstractSpimData< ?, AS > io, final FilteredAndGroupedExplorer< AS > viewSetupExplorer ) { this.xml = xml; this.viewSetupExplorer = viewSetupExplorer; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorerPanel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorerPanel.java index 99c51f36a..3a6ef3ac2 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorerPanel.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorerPanel.java @@ -77,9 +77,9 @@ public class RegistrationExplorerPanel extends JPanel { private static final long serialVersionUID = -3767947754096099774L; - - final RegistrationExplorer< ?, ? > explorer; - + + final RegistrationExplorer< ? > explorer; + protected JTable table; protected RegistrationTableModel tableModel; protected JLabel label; @@ -89,8 +89,8 @@ public class RegistrationExplorerPanel extends JPanel protected List> lastSelectedVDs; protected ArrayList< ViewTransform > cache; - - public RegistrationExplorerPanel( final ViewRegistrations viewRegistrations, final RegistrationExplorer< ?, ? > explorer ) + + public RegistrationExplorerPanel( final ViewRegistrations viewRegistrations, final RegistrationExplorer< ? > explorer ) { this.cache = new ArrayList< ViewTransform >(); this.explorer = explorer; diff --git a/src/main/java/net/preibisch/mvrecon/headless/splitting/TestSplitting.java b/src/main/java/net/preibisch/mvrecon/headless/splitting/TestSplitting.java index d973cb432..70787f324 100644 --- a/src/main/java/net/preibisch/mvrecon/headless/splitting/TestSplitting.java +++ b/src/main/java/net/preibisch/mvrecon/headless/splitting/TestSplitting.java @@ -60,7 +60,7 @@ public static void main( String[] args ) throws SpimDataException SpimData2 newSD = SplittingTools.splitImages( spimData, new long[] { 30, 30, 10 }, new long[] { 200, 200, 40 } ); // drosophila with 1000 views - final ViewSetupExplorer< SpimData2, XmlIoSpimData2 > explorer = new ViewSetupExplorer( newSD, fileOut, new XmlIoSpimData2( "" ) ); + final ViewSetupExplorer< SpimData2 > explorer = new ViewSetupExplorer<>( newSD, fileOut, new XmlIoSpimData2( "" ) ); explorer.getFrame().toFront(); } From 1fe4f80b6df2b7186053d3bea0c5af0dc39b9e16 Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Sat, 11 Nov 2023 15:20:19 +0100 Subject: [PATCH 08/13] Formatting and minor simplifications (no functional change) --- .../FilteredAndGroupedExplorerPanel.java | 262 ++++++++---------- 1 file changed, 108 insertions(+), 154 deletions(-) diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java index 2e74f3ffa..1ec7b5413 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java @@ -22,6 +22,7 @@ */ package net.preibisch.mvrecon.fiji.spimdata.explorer; +import java.awt.event.KeyAdapter; import java.awt.event.KeyEvent; import java.awt.event.KeyListener; import java.util.ArrayList; @@ -69,7 +70,7 @@ import net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPoints; import net.preibisch.mvrecon.process.interestpointregistration.TransformationTools; -public abstract class FilteredAndGroupedExplorerPanel > +public abstract class FilteredAndGroupedExplorerPanel< AS extends AbstractSpimData< ? > > extends JPanel implements ExplorerWindow< AS >, GroupedRowWindow { public static FilteredAndGroupedExplorerPanel< ? > currentInstance = null; @@ -81,8 +82,8 @@ public abstract class FilteredAndGroupedExplorerPanel explorer, final AS data, final String xml, final XmlIoAbstractSpimData< ?, AS > io) { - - - + + + this.explorer = explorer; - this.listeners = new ArrayList< SelectedViewDescriptionListener< AS > >(); + this.listeners = new ArrayList<>(); this.data = data; // normalize the xml path @@ -118,9 +119,9 @@ public FilteredAndGroupedExplorerPanel(final FilteredAndGroupedExplorer< AS > ex this.selectedRows = new HashSet<>(); this.firstSelectedVD = null; - + popups = initPopups(); - + // for access to the current BDV currentInstance = this; } @@ -129,8 +130,8 @@ public FilteredAndGroupedExplorerPanel(final FilteredAndGroupedExplorer< AS > ex public BDVPopup bdvPopup() { for ( final ExplorerWindowSetable s : popups ) - if ( BDVPopup.class.isInstance( s ) ) - return ( (BDVPopup) s ); + if ( s instanceof BDVPopup ) + return ( BDVPopup ) s; return null; } @@ -142,7 +143,7 @@ public boolean colorMode() } @Override - public BasicViewDescription< ? extends BasicViewSetup > firstSelectedVD() + public BasicViewDescription< ? > firstSelectedVD() { return firstSelectedVD; } @@ -174,10 +175,10 @@ public FilteredAndGroupedExplorer< AS > explorer() return explorer; } - @SuppressWarnings("unchecked") - public void setSpimData(final Object data) + @SuppressWarnings( "unchecked" ) + public void setSpimData( final Object data ) { - this.data = (AS) data; + this.data = ( AS ) data; this.getTableModel().updateElements(); } @@ -190,11 +191,11 @@ public void updateContent() } @Override - public List< BasicViewDescription< ? extends BasicViewSetup > > selectedRows() + public List< BasicViewDescription< ? > > selectedRows() { // TODO: this will break the grouping of selected Views -> change interface??? - final ArrayList< BasicViewDescription< ? extends BasicViewSetup > > list = new ArrayList< BasicViewDescription< ? extends BasicViewSetup > >(); - for (List> vds : selectedRows) + final ArrayList< BasicViewDescription< ? > > list = new ArrayList<>(); + for ( List< BasicViewDescription< ? > > vds : selectedRows ) list.addAll( vds ); Collections.sort( list ); return list; @@ -204,13 +205,9 @@ public void updateContent() public List< ViewId > selectedRowsViewId() { // TODO: adding Grouped Views here, not all selected ViewIds individually - final ArrayList< ViewId > list = new ArrayList< ViewId >(); - for (List> vds : selectedRows) - { - ArrayList< ViewId > vids = new ArrayList<>(); - vids.addAll( vds ); - list.add( new GroupedViews( vids )); - } + final ArrayList< ViewId > list = new ArrayList<>(); + for ( List< BasicViewDescription< ? > > vds : selectedRows ) + list.add( new GroupedViews( new ArrayList<>( vds ) ) ); Collections.sort( list ); return list; } @@ -219,10 +216,7 @@ public void addListener(final SelectedViewDescriptionListener< AS > listener) { this.listeners.add( listener ); - List>> selectedList = new ArrayList<>(); - for (List> selectedI : selectedRows) - selectedList.add( selectedI ); - + final List< List< BasicViewDescription< ? > > > selectedList = new ArrayList<>( selectedRows ); listener.selectedViewDescriptions( selectedList ); } @@ -232,48 +226,43 @@ public ArrayList< SelectedViewDescriptionListener< AS > > getListeners() } public abstract void initComponent(); - - public void updateFilter(Class entityClass, Entity selectedInstance) + + public void updateFilter( Class< ? extends Entity > entityClass, Entity selectedInstance ) { - ArrayList selectedInstances = new ArrayList<>(); + ArrayList< Entity > selectedInstances = new ArrayList<>(); selectedInstances.add( selectedInstance ); tableModel.addFilter( entityClass, selectedInstances ); } - - protected static List getEntityNamesOrIds(List entities) + + protected static List< String > getEntityNamesOrIds( List< ? extends Entity > entities ) { - ArrayList names = new ArrayList<>(); - - for (Entity e : entities) - names.add( NamedEntity.class.isInstance( e ) ? ((NamedEntity)e).getName() : Integer.toString( e.getId())); - + ArrayList< String > names = new ArrayList<>(); + + for ( Entity e : entities ) + names.add( e instanceof NamedEntity ? ( ( NamedEntity ) e ).getName() : Integer.toString( e.getId() ) ); + return names; } - - public static Entity getInstanceFromNameOrId(AbstractSequenceDescription sd, Class entityClass, String nameOrId) + + public static Entity getInstanceFromNameOrId( AbstractSequenceDescription< ?, ?, ? > sd, Class< ? extends Entity > entityClass, String nameOrId ) { - for (Entity e : SpimDataTools.getInstancesOfAttribute( sd, entityClass )) - if (NamedEntity.class.isInstance( e ) && ((NamedEntity)e).getName().equals( nameOrId ) || Integer.toString( e.getId()).equals( nameOrId )) + for ( Entity e : SpimDataTools.getInstancesOfAttribute( sd, entityClass ) ) + if ( e instanceof NamedEntity && ( ( NamedEntity ) e ).getName().equals( nameOrId ) || Integer.toString( e.getId() ).equals( nameOrId ) ) return e; return null; } protected void addHelp() { - table.addKeyListener( new KeyListener() + table.addKeyListener( new KeyAdapter() + { + @Override + public void keyPressed( KeyEvent e ) { - public void keyTyped( KeyEvent e ) {} - - @Override - public void keyReleased( KeyEvent e ) {} - - @Override - public void keyPressed( KeyEvent e ) - { - if ( e.getKeyCode() == 112 ) - new HelpDialog( explorer().getFrame(), this.getClass().getResource( getHelpHtml() ) ).setVisible( true ); - } - } ); + if ( e.getKeyCode() == 112 ) + new HelpDialog( explorer().getFrame(), this.getClass().getResource( getHelpHtml() ) ).setVisible( true ); + } + } ); } protected abstract String getHelpHtml(); @@ -298,15 +287,15 @@ public void valueChanged(final ListSelectionEvent arg0) selectedRows.add( tableModel.getElements().get( row ) ); } - + List>> selectedList = new ArrayList<>(); for (List> selectedI : selectedRows) selectedList.add( selectedI ); - + for ( int i = 0; i < listeners.size(); ++i ) listeners.get( i ).selectedViewDescriptions( selectedList ); - + /* if ( table.getSelectedRowCount() != 1 ) { @@ -354,47 +343,47 @@ public void valueChanged(final ListSelectionEvent arg0) */ if ( b != null && b.bdv != null ) - { + { updateBDV( b.bdv, colorMode, data, firstSelectedVD, selectedRows); - + } - - + + } - + }; } - - - - public static void resetBDVManualTransformations(BigDataViewer bdv) + public static void resetBDVManualTransformations( BigDataViewer bdv ) { if ( bdv == null ) return; - + // reset manual transform for all views - for (int sourceIdx = 0; sourceIdx s = bdv.getViewer().getVisibilityAndGrouping().getSources().get( sourceIdx ); - ((TransformedSource< ? >)s.getSpimSource()).setFixedTransform( new AffineTransform3D() ); - ((TransformedSource< ? >)s.getSpimSource()).setIncrementalTransform( new AffineTransform3D() ); + SourceState< ? > s = bdv.getViewer().getVisibilityAndGrouping().getSources().get( sourceIdx ); + ( ( TransformedSource< ? > ) s.getSpimSource() ).setFixedTransform( new AffineTransform3D() ); + ( ( TransformedSource< ? > ) s.getSpimSource() ).setIncrementalTransform( new AffineTransform3D() ); } } - - public static void updateBDV(final BigDataViewer bdv, final boolean colorMode, final AbstractSpimData< ? > data, + + public static void updateBDV( + final BigDataViewer bdv, + final boolean colorMode, + final AbstractSpimData< ? > data, BasicViewDescription< ? extends BasicViewSetup > firstVD, final Collection< List< BasicViewDescription< ? > > > selectedRows ) { - + // bdv is not open if ( bdv == null ) return; - + // we always set the fused mode //setFusedModeSimple( bdv, data ); - + //resetBDVManualTransformations( bdv ); if ( selectedRows == null || selectedRows.size() == 0 ) @@ -425,51 +414,48 @@ public static void updateBDV(final BigDataViewer bdv, final boolean colorMode, f bdv.getViewer().requestRepaint(); } - public static void setFusedModeSimple(final BigDataViewer bdv, final AbstractSpimData< ? > data) + public static void setFusedModeSimple( final BigDataViewer bdv, final AbstractSpimData< ? > data ) { if ( bdv == null ) return; - - if ( bdv.getViewer().getVisibilityAndGrouping().getDisplayMode() != DisplayMode.FUSED ) { - final boolean[] active = new boolean[data.getSequenceDescription().getViewSetupsOrdered().size()]; - active[0] = true; + final boolean[] active = new boolean[ data.getSequenceDescription().getViewSetupsOrdered().size() ]; + active[ 0 ] = true; setVisibleSources( bdv.getViewer().getVisibilityAndGrouping(), active ); bdv.getViewer().getVisibilityAndGrouping().setDisplayMode( DisplayMode.FUSED ); } } - public static void colorSources(final List< ConverterSetup > cs, AbstractSpimData< ? > data, Map channelColors) + public static void colorSources( final List< ConverterSetup > cs, AbstractSpimData< ? > data, Map< Channel, ARGBType > channelColors ) { for ( int i = 0; i < cs.size(); ++i ) - { - Channel ch = data.getSequenceDescription().getViewSetups().get(cs.get( i ).getSetupId()).getAttribute( Channel.class ); + { + Channel ch = data.getSequenceDescription().getViewSetups().get( cs.get( i ).getSetupId() ).getAttribute( Channel.class ); cs.get( i ).setColor( channelColors.get( ch ) ); } } - public static void whiteSources(final List< ConverterSetup > cs) + public static void whiteSources( final List< ConverterSetup > cs ) { for ( int i = 0; i < cs.size(); ++i ) cs.get( i ).setColor( new ARGBType( ARGBType.rgba( 255, 255, 255, 255 ) ) ); } - public static void sameColorSources(final List< ConverterSetup > cs, final int r, final int g, final int b, final int a) + public static void sameColorSources( final List< ConverterSetup > cs, final int r, final int g, final int b, final int a ) { for ( int i = 0; i < cs.size(); ++i ) cs.get( i ).setColor( new ARGBType( ARGBType.rgba( r, g, b, a ) ) ); } - public static void setVisibleSources(final VisibilityAndGrouping vag, final boolean[] active) + public static void setVisibleSources( final VisibilityAndGrouping vag, final boolean[] active ) { for ( int i = 0; i < active.length; ++i ) - vag.setSourceActive( i, active[i] ); - + vag.setSourceActive( i, active[ i ] ); } - public static int getBDVTimePointIndex(final TimePoint t, final AbstractSpimData< ? > data) + public static int getBDVTimePointIndex( final TimePoint t, final AbstractSpimData< ? > data ) { final List< TimePoint > list = data.getSequenceDescription().getTimePoints().getTimePointsOrdered(); @@ -480,7 +466,7 @@ public static int getBDVTimePointIndex(final TimePoint t, final AbstractSpimData return 0; } - public static int getBDVSourceIndex(final BasicViewSetup vs, final AbstractSpimData< ? > data) + public static int getBDVSourceIndex( final BasicViewSetup vs, final AbstractSpimData< ? > data ) { final List< ? extends BasicViewSetup > list = data.getSequenceDescription().getViewSetupsOrdered(); @@ -491,14 +477,14 @@ public static int getBDVSourceIndex(final BasicViewSetup vs, final AbstractSpimD return 0; } - public HashSet< List >> getSelectedRows() + public HashSet< List< BasicViewDescription< ? extends BasicViewSetup > > > getSelectedRows() { return selectedRows; } public void showInfoBox() { - new ViewSetupExplorerInfoBox< AS >( data, xml ); + new ViewSetupExplorerInfoBox<>( data, xml ); } @Override @@ -511,9 +497,9 @@ public void saveXML() for ( final SelectedViewDescriptionListener< AS > l : listeners ) l.save(); - if ( SpimData2.class.isInstance( data ) ) + if ( data instanceof SpimData2 ) { - final ViewInterestPoints vip = ( (SpimData2) data ).getViewInterestPoints(); + final ViewInterestPoints vip = ( ( SpimData2 ) data ).getViewInterestPoints(); for ( final ViewInterestPointLists vipl : vip.getViewInterestPoints().values() ) { @@ -535,7 +521,7 @@ public void saveXML() } } - protected void addPopupMenu(final JTable table) + protected void addPopupMenu( final JTable table ) { final JPopupMenu popupMenu = new JPopupMenu(); @@ -547,10 +533,10 @@ protected void addPopupMenu(final JTable table) protected void addColorMode() { - table.addKeyListener( new KeyListener() + table.addKeyListener( new KeyAdapter() { @Override - public void keyPressed(final KeyEvent arg0) + public void keyPressed( final KeyEvent arg0 ) { if ( arg0.getKeyChar() == 'c' || arg0.getKeyChar() == 'C' ) { @@ -560,28 +546,18 @@ public void keyPressed(final KeyEvent arg0) final BDVPopup p = bdvPopup(); if ( p != null && p.bdv != null && p.bdv.getViewerFrame().isVisible() ) - updateBDV( p.bdv, colorMode, data, null, selectedRows); + updateBDV( p.bdv, colorMode, data, null, selectedRows ); } } - - @Override - public void keyReleased(final KeyEvent arg0) - { - } - - @Override - public void keyTyped(final KeyEvent arg0) - { - } } ); } protected void addReCenterShortcut() { - table.addKeyListener( new KeyListener() + table.addKeyListener( new KeyAdapter() { @Override - public void keyPressed(final KeyEvent arg0) + public void keyPressed( final KeyEvent arg0 ) { if ( arg0.getKeyChar() == 'r' || arg0.getKeyChar() == 'R' ) { @@ -589,18 +565,13 @@ public void keyPressed(final KeyEvent arg0) if ( p != null && p.bdv != null && p.bdv.getViewerFrame().isVisible() ) { TransformationTools.reCenterViews( p.bdv, - selectedRows.stream().collect( + selectedRows.stream().collect( HashSet< BasicViewDescription< ? > >::new, - (a, b) -> a.addAll( b ), (a, b) -> a.addAll( b ) ), - data.getViewRegistrations() ); + ( a, b ) -> a.addAll( b ), ( a, b ) -> a.addAll( b ) ), + data.getViewRegistrations() ); } } } - - @Override - public void keyReleased(final KeyEvent arg0){} - @Override - public void keyTyped(final KeyEvent arg0){} } ); } @@ -611,21 +582,21 @@ protected void addAppleA() boolean appleKeyDown = false; @Override - public void keyTyped(KeyEvent arg0) + public void keyTyped( KeyEvent arg0 ) { if ( appleKeyDown && arg0.getKeyChar() == 'a' ) table.selectAll(); } @Override - public void keyReleased(KeyEvent arg0) + public void keyReleased( KeyEvent arg0 ) { if ( arg0.getKeyCode() == 157 ) appleKeyDown = false; } @Override - public void keyPressed(KeyEvent arg0) + public void keyPressed( KeyEvent arg0 ) { if ( arg0.getKeyCode() == 157 ) appleKeyDown = true; @@ -637,17 +608,17 @@ public void keyPressed(KeyEvent arg0) protected void addScreenshot() { - table.addKeyListener( new KeyListener() + table.addKeyListener( new KeyAdapter() { @Override - public void keyPressed(final KeyEvent arg0) + public void keyPressed( final KeyEvent arg0 ) { if ( arg0.getKeyChar() == 'E' ) { enableFlyThrough = true; IOFunctions.println( "EASTER EGG activated." ); - IOFunctions.println( "You can now record a fly-through: "); + IOFunctions.println( "You can now record a fly-through: " ); IOFunctions.println( " press 'a' to add the current view as keypoint" ); IOFunctions.println( " press 'x' to remove all keypoints" ); IOFunctions.println( " press 'd' to remove last keypoint" ); @@ -672,13 +643,13 @@ public void run() } ).start(); else IOFunctions.println("Please open BigDataViewer to record a fly-through or add keypoints."); - + if ( arg0.getKeyChar() == 'a' ) if (bdvRunning) BDVFlyThrough.addCurrentViewerTransform( bdvPopup().bdv.getViewer() ); else IOFunctions.println("Please open BigDataViewer to record a fly-through or add keypoints."); - + if ( arg0.getKeyChar() == 'x' ) BDVFlyThrough.clearAllViewerTransform(); @@ -688,32 +659,19 @@ public void run() if ( arg0.getKeyChar() == 'j' ) BDVFlyThrough.jumpToLastViewerTransform( bdvPopup().bdv.getViewer() ); - if ( arg0.getKeyChar() == 's' ) { + if ( arg0.getKeyChar() == 's' ) try { BDVFlyThrough.saveViewerTransforms(); } catch ( Exception e ) { IOFunctions.println( "couldn't save json: " + e ); } - } - if ( arg0.getKeyChar() == 'l' ){ + if ( arg0.getKeyChar() == 'l' ) try { BDVFlyThrough.loadViewerTransforms(); } catch ( Exception e ) { IOFunctions.println( "couldn't load json: " + e ); } - } if ( arg0.getKeyChar() == 'R' ) - if (bdvRunning) - new Thread( new Runnable() - { - @Override - public void run() - { BDVFlyThrough.renderScreenshot( bdvPopup().bdv.getViewer() ); } - } ).start(); + if ( bdvRunning ) + new Thread( () -> BDVFlyThrough.renderScreenshot( bdvPopup().bdv.getViewer() ) ).start(); else - IOFunctions.println("Please open BigDataViewer to make a screenshot."); + IOFunctions.println( "Please open BigDataViewer to make a screenshot." ); } } - - @Override - public void keyReleased(final KeyEvent arg0) {} - - @Override - public void keyTyped(final KeyEvent arg0){} } ); } @@ -728,13 +686,9 @@ public void keyTyped(final KeyEvent arg0){} @Override public List< List< ViewId > > selectedRowsViewIdGroups() { - final ArrayList< List> list = new ArrayList<>(); - for (List> vds : selectedRows) - { - ArrayList< ViewId > vids = new ArrayList<>(); - vids.addAll( vds ); - list.add( vids); - } + final ArrayList< List< ViewId > > list = new ArrayList<>(); + for ( List< BasicViewDescription< ? > > vds : selectedRows ) + list.add( new ArrayList<>( vds ) ); //Collections.sort( list ); return list; } From 9ee43d0d844658f06ddf6190df5eecb0159ecbcd Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Sun, 12 Nov 2023 21:33:21 +0100 Subject: [PATCH 09/13] Simplify generics --- .../datasetmanager/grid/RegularTranformHelpers.java | 8 ++++---- .../explorer/FilteredAndGroupedExplorerPanel.java | 9 +++++---- .../explorer/FilteredAndGroupedTableModel.java | 10 +++++----- .../explorer/MultiViewTableModelDecorator.java | 2 +- .../fiji/spimdata/explorer/ViewSetupExplorerPanel.java | 10 +++++----- .../explorer/interestpoint/InterestPointExplorer.java | 8 ++++---- .../interestpoint/InterestPointExplorerPanel.java | 8 ++++---- .../explorer/registration/RegistrationExplorer.java | 6 +++--- .../mvrecon/fiji/spimdata/imgloaders/DHMImgLoader.java | 2 +- .../fiji/spimdata/imgloaders/LegacyDHMImgLoader.java | 4 ++-- .../imgloaders/LegacyMicroManagerImgLoader.java | 4 ++-- .../spimdata/imgloaders/MicroManagerImgLoader.java | 2 +- .../process/deconvolution/util/ProcessInputImages.java | 10 +++++----- .../preibisch/mvrecon/process/fusion/FusionTools.java | 6 +++--- 14 files changed, 45 insertions(+), 44 deletions(-) diff --git a/src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/grid/RegularTranformHelpers.java b/src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/grid/RegularTranformHelpers.java index 89eefedab..ddf4e5bff 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/grid/RegularTranformHelpers.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/grid/RegularTranformHelpers.java @@ -264,8 +264,8 @@ private static int prod(int ... v) } public static > void applyToSpimData( - AS data, - List > > viewDescriptions, + AS data, + List > > viewDescriptions, RegularTranslationParameters params, boolean applyToAllTimePoints) { @@ -313,8 +313,8 @@ private static int getRotationAxisFromUnitVector(double[] axis) } private static > void applyToSpimDataSingleTP( - AS data, - List< ? extends Group< ? extends BasicViewDescription< ? extends BasicViewSetup > > > viewDescriptions, + AS data, + List< ? extends Group< ? extends BasicViewDescription< ? > > > viewDescriptions, RegularTranslationParameters params, TimePoint tp) { diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java index 1ec7b5413..a3b358b9e 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java @@ -32,6 +32,7 @@ import java.util.List; import java.util.Map; +import java.util.Set; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JTable; @@ -97,7 +98,7 @@ public abstract class FilteredAndGroupedExplorerPanel< AS extends AbstractSpimDa protected boolean colorMode = false; final protected HashSet< List< BasicViewDescription< ? > > > selectedRows; - protected BasicViewDescription< ? extends BasicViewSetup > firstSelectedVD; + protected BasicViewDescription< ? > firstSelectedVD; public FilteredAndGroupedExplorerPanel(final FilteredAndGroupedExplorer< AS > explorer, final AS data, final String xml, final XmlIoAbstractSpimData< ?, AS > io) @@ -373,7 +374,7 @@ public static void updateBDV( final BigDataViewer bdv, final boolean colorMode, final AbstractSpimData< ? > data, - BasicViewDescription< ? extends BasicViewSetup > firstVD, + BasicViewDescription< ? > firstVD, final Collection< List< BasicViewDescription< ? > > > selectedRows ) { @@ -399,7 +400,7 @@ public static void updateBDV( final boolean[] active = new boolean[data.getSequenceDescription().getViewSetupsOrdered().size()]; - for ( final List< ? extends BasicViewDescription< ? extends BasicViewSetup > > vds : selectedRows ) + for ( final List< ? extends BasicViewDescription< ? > > vds : selectedRows ) for ( BasicViewDescription< ? > vd : vds){ if ( vd.getTimePointId() == firstTP.getId() ) active[getBDVSourceIndex( vd.getViewSetup(), data )] = true; @@ -477,7 +478,7 @@ public static int getBDVSourceIndex( final BasicViewSetup vs, final AbstractSpim return 0; } - public HashSet< List< BasicViewDescription< ? extends BasicViewSetup > > > getSelectedRows() + public Set< List< BasicViewDescription< ? > > > getSelectedRows() { return selectedRows; } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedTableModel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedTableModel.java index c6a7dce09..86543af1b 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedTableModel.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedTableModel.java @@ -170,12 +170,12 @@ public FilteredAndGroupedTableModel( final ExplorerWindow< AS > panel ) elements(); } - protected List >> elements() + protected List >> elements() { return elements(false); } - protected List >> elements( boolean forceUpdate ) + protected List >> elements( boolean forceUpdate ) { if (!forceUpdate && elements != null) return elements; @@ -235,12 +235,12 @@ public boolean isCellEditable( final int row, final int column ) @Override public Object getValueAt( final int row, final int column ) { - final List> vds = elements().get( row ); + final List> vds = elements().get( row ); Class c = columnClasses.get(column); final HashSet entries = new HashSet<>(); - - for (BasicViewDescription< ? extends BasicViewSetup > vd : vds) + + for (BasicViewDescription< ? > vd : vds) { if ( c == TimePoint.class ) entries.add(vd.getTimePoint()); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MultiViewTableModelDecorator.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MultiViewTableModelDecorator.java index f24cf1d92..d1d07e7cd 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MultiViewTableModelDecorator.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/MultiViewTableModelDecorator.java @@ -124,7 +124,7 @@ public Object getValueAt(int rowIndex, int columnIndex) { if ( vds.size() == 1 ) { - final BasicViewDescription< ? extends BasicViewSetup > vd = vds.get( 0 ); + final BasicViewDescription< ? > vd = vds.get( 0 ); if ( vd.isPresent() ) { diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorerPanel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorerPanel.java index 5a90e4a15..e959dc220 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorerPanel.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/ViewSetupExplorerPanel.java @@ -344,9 +344,9 @@ public void valueChanged(final ListSelectionEvent arg0) selectedRows.add( tableModel.getElements().get( row ) ); } - - List>> selectedList = new ArrayList<>(); - for (List> selectedI : selectedRows) + + List>> selectedList = new ArrayList<>(); + for (List> selectedI : selectedRows) selectedList.add( selectedI ); for ( int i = 0; i < listeners.size(); ++i ) @@ -415,8 +415,8 @@ public void valueChanged(final ListSelectionEvent arg0) } public static void updateBDV(final BigDataViewer bdv, final boolean colorMode, final AbstractSpimData< ? > data, - BasicViewDescription< ? extends BasicViewSetup > firstVD, - final Collection< List< BasicViewDescription< ? extends BasicViewSetup >> > selectedRows) + BasicViewDescription< ? > firstVD, + final Collection< List< BasicViewDescription< ? >> > selectedRows) { // we always set the fused mode setFusedModeSimple( bdv, data ); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorer.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorer.java index d9fede760..f8481e8d7 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorer.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorer.java @@ -91,12 +91,12 @@ public void windowClosing(WindowEvent e) public JFrame frame() { return frame; } @Override - public void selectedViewDescriptions( final List< List< BasicViewDescription< ? extends BasicViewSetup > > > viewDescriptions ) + public void selectedViewDescriptions( final List< List< BasicViewDescription< ? > > > viewDescriptions ) { - final ArrayList< BasicViewDescription< ? extends BasicViewSetup > > fullList = new ArrayList<>(); + final ArrayList< BasicViewDescription< ? > > fullList = new ArrayList<>(); - for ( final List< BasicViewDescription< ? extends BasicViewSetup > > list : viewDescriptions ) - for ( final BasicViewDescription< ? extends BasicViewSetup > vd : list ) + for ( final List< BasicViewDescription< ? > > list : viewDescriptions ) + for ( final BasicViewDescription< ? > vd : list ) if ( vd.isPresent() ) fullList.add( vd ); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorerPanel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorerPanel.java index ba140f75c..ebd8ba096 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorerPanel.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/interestpoint/InterestPointExplorerPanel.java @@ -84,12 +84,12 @@ public InterestPointExplorerPanel( final ViewInterestPoints viewInterestPoints, public InterestPointTableModel getTableModel() { return tableModel; } public JTable getTable() { return table; } - - public void updateViewDescription( final List< BasicViewDescription< ? extends BasicViewSetup > > viewDescriptionsUnfiltered ) + + public void updateViewDescription( final List< BasicViewDescription< ? > > viewDescriptionsUnfiltered ) { - final ArrayList< BasicViewDescription< ? extends BasicViewSetup > > viewDescriptions = new ArrayList<>(); + final ArrayList< BasicViewDescription< ? > > viewDescriptions = new ArrayList<>(); - for ( final BasicViewDescription< ? extends BasicViewSetup > vd : viewDescriptionsUnfiltered ) + for ( final BasicViewDescription< ? > vd : viewDescriptionsUnfiltered ) if ( vd.isPresent() ) viewDescriptions.add( vd ); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorer.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorer.java index d5a531754..2dd8f3056 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorer.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/registration/RegistrationExplorer.java @@ -78,10 +78,10 @@ public RegistrationExplorer( final String xml, final XmlIoAbstractSpimData< ?, A public void save() {} @Override - public void selectedViewDescriptions( final List >> viewDescriptions ) + public void selectedViewDescriptions( final List >> viewDescriptions ) { - List> vdsFlat = new ArrayList<>(); - for (List> vdsI : viewDescriptions) + List> vdsFlat = new ArrayList<>(); + for (List> vdsI : viewDescriptions) vdsFlat.addAll( vdsI ); panel.updateViewDescriptions( vdsFlat ); System.out.println( viewDescriptions ); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/DHMImgLoader.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/DHMImgLoader.java index a84867e68..bd43ac29d 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/DHMImgLoader.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/DHMImgLoader.java @@ -43,7 +43,7 @@ public DHMImgLoader( final String extension, final int ampChannelId, final int phaseChannelId, - final AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? > sd ) + final AbstractSequenceDescription< ?, ?, ? > sd ) { super( new LegacyDHMImgLoader( directory, stackDir, amplitudeDir, phaseDir, timepoints, zPlanes, extension, ampChannelId, phaseChannelId, sd ) ); } diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyDHMImgLoader.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyDHMImgLoader.java index b1950fdeb..7ee55a99d 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyDHMImgLoader.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyDHMImgLoader.java @@ -51,7 +51,7 @@ public class LegacyDHMImgLoader extends AbstractImgLoader { final File directory; - final AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? > sd; + final AbstractSequenceDescription< ?, ?, ? > sd; final List< String > timepoints; final List< String > zPlanes; final String stackDir; @@ -71,7 +71,7 @@ public LegacyDHMImgLoader( final String extension, final int ampChannelId, final int phaseChannelId, - final AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? > sd ) + final AbstractSequenceDescription< ?, ?, ? > sd ) { this.directory = directory; this.stackDir = stackDir; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyMicroManagerImgLoader.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyMicroManagerImgLoader.java index 78a06fdf3..d3f68cb77 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyMicroManagerImgLoader.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/LegacyMicroManagerImgLoader.java @@ -53,11 +53,11 @@ public class LegacyMicroManagerImgLoader extends AbstractImgLoader { final File mmFile; - final AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? > sequenceDescription; + final AbstractSequenceDescription< ?, ?, ? > sequenceDescription; public LegacyMicroManagerImgLoader( final File mmFile, - final AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? > sequenceDescription ) + final AbstractSequenceDescription< ?, ?, ? > sequenceDescription ) { super(); this.mmFile = mmFile; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/MicroManagerImgLoader.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/MicroManagerImgLoader.java index 8739523e1..77bf3d6be 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/MicroManagerImgLoader.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/imgloaders/MicroManagerImgLoader.java @@ -34,7 +34,7 @@ public class MicroManagerImgLoader extends LegacyImgLoaderWrapper< UnsignedShort { public MicroManagerImgLoader( final File mmFile, - final AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? > sequenceDescription ) + final AbstractSequenceDescription< ?, ?, ? > sequenceDescription ) { super( new LegacyMicroManagerImgLoader( mmFile, sequenceDescription ) ); } diff --git a/src/main/java/net/preibisch/mvrecon/process/deconvolution/util/ProcessInputImages.java b/src/main/java/net/preibisch/mvrecon/process/deconvolution/util/ProcessInputImages.java index 004505b33..f8b1702a3 100644 --- a/src/main/java/net/preibisch/mvrecon/process/deconvolution/util/ProcessInputImages.java +++ b/src/main/java/net/preibisch/mvrecon/process/deconvolution/util/ProcessInputImages.java @@ -66,7 +66,7 @@ public class ProcessInputImages< V extends ViewId > { - final AbstractSpimData< ? extends AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? extends BasicImgLoader > > spimData; + final AbstractSpimData< ? > spimData; final ArrayList< Group< V > > groups; final Interval bb; Interval downsampledBB; @@ -81,7 +81,7 @@ public class ProcessInputImages< V extends ViewId > final Map< ? extends ViewId, AffineModel1D > intensityAdjustments; public ProcessInputImages( - final AbstractSpimData< ? extends AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? extends BasicImgLoader > > spimData, + final AbstractSpimData< ? > spimData, final Collection< Group< V > > groups, final ExecutorService service, final Interval bb, @@ -116,7 +116,7 @@ public ProcessInputImages( } public ProcessInputImages( - final AbstractSpimData< ? extends AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? extends BasicImgLoader > > spimData, + final AbstractSpimData< ? > spimData, final Collection< Group< V > > groups, final ExecutorService service, final Interval bb, @@ -131,7 +131,7 @@ public ProcessInputImages( } public ProcessInputImages( - final AbstractSpimData< ? extends AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? extends BasicImgLoader > > spimData, + final AbstractSpimData< ? > spimData, final Collection< Group< V > > groups, final ExecutorService service, final Interval bb, @@ -275,7 +275,7 @@ public static < V extends ViewId > void copyRandomAccessibleInterval( } public static < V extends ViewId > Interval fuseGroups( - final AbstractSpimData< ? extends AbstractSequenceDescription< ? extends BasicViewSetup, ? extends BasicViewDescription< ? >, ? extends BasicImgLoader > > spimData, + final AbstractSpimData< ? > spimData, final HashMap< Group< V >, RandomAccessibleInterval< FloatType > > tImgs, final HashMap< Group< V >, RandomAccessibleInterval< FloatType > > tWeights, final HashMap< V, AffineTransform3D > models, diff --git a/src/main/java/net/preibisch/mvrecon/process/fusion/FusionTools.java b/src/main/java/net/preibisch/mvrecon/process/fusion/FusionTools.java index d00cf694c..1cdca1b86 100644 --- a/src/main/java/net/preibisch/mvrecon/process/fusion/FusionTools.java +++ b/src/main/java/net/preibisch/mvrecon/process/fusion/FusionTools.java @@ -662,7 +662,7 @@ else if ( imgType == ImgDataType.PRECOMPUTED ) * @param border - the target blending border, e.g. 0 * @param transformationModel - the transformation model used to map from the (downsampled) input to the output */ - public static void adjustBlending( final BasicViewDescription< ? extends BasicViewSetup > vd, final float[] blending, final float[] border, final AffineTransform3D transformationModel ) + public static void adjustBlending( final BasicViewDescription< ? > vd, final float[] blending, final float[] border, final AffineTransform3D transformationModel ) { adjustBlending( vd.getViewSetup().getSize(), Group.pvid( vd ), blending, border, transformationModel ); } @@ -691,7 +691,7 @@ public static void adjustBlending( final Dimensions dim, final String name, fina * @param sigma2 - the target sigma2 for entropy approximation, e.g. 40 * @param usedDownsampleFactors - the downsampling factors used to load the input image */ - public static void adjustContentBased( final BasicViewDescription< ? extends BasicViewSetup > vd, final double[] sigma1, final double[] sigma2, final double[] usedDownsampleFactors ) + public static void adjustContentBased( final BasicViewDescription< ? > vd, final double[] sigma1, final double[] sigma2, final double[] usedDownsampleFactors ) { for ( int d = 0; d < sigma1.length; ++d ) { @@ -700,7 +700,7 @@ public static void adjustContentBased( final BasicViewDescription< ? extends Bas } } - public static double getMinRes( final BasicViewDescription< ? extends BasicViewSetup > desc ) + public static double getMinRes( final BasicViewDescription< ? > desc ) { final VoxelDimensions size = ViewSetupUtils.getVoxelSize( desc.getViewSetup() ); From 3c1433eb31998998d41aac9eacc04aaf4412354a Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Thu, 16 Nov 2023 15:48:42 +0100 Subject: [PATCH 10/13] Fix usage of deprecated API in FilteredAndGroupedExplorerPanel --- .../FilteredAndGroupedExplorerPanel.java | 88 ++++++++++--------- .../fiji/spimdata/explorer/bdv/BDVUtils.java | 40 +++++++++ 2 files changed, 88 insertions(+), 40 deletions(-) create mode 100644 src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/bdv/BDVUtils.java diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java index a3b358b9e..351a31b31 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/FilteredAndGroupedExplorerPanel.java @@ -30,9 +30,9 @@ import java.util.Collections; import java.util.HashSet; import java.util.List; -import java.util.Map; import java.util.Set; +import java.util.stream.Collectors; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.JTable; @@ -42,10 +42,9 @@ import bdv.BigDataViewer; import bdv.tools.HelpDialog; import bdv.tools.brightness.ConverterSetup; -import bdv.tools.transformation.TransformedSource; import bdv.viewer.DisplayMode; -import bdv.viewer.VisibilityAndGrouping; -import bdv.viewer.state.SourceState; +import bdv.viewer.SourceAndConverter; +import bdv.viewer.ViewerState; import mpicbg.spim.data.SpimDataException; import mpicbg.spim.data.generic.AbstractSpimData; import mpicbg.spim.data.generic.XmlIoAbstractSpimData; @@ -64,6 +63,7 @@ import net.preibisch.mvrecon.fiji.spimdata.SpimData2; import net.preibisch.mvrecon.fiji.spimdata.SpimDataTools; import net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVFlyThrough; +import net.preibisch.mvrecon.fiji.spimdata.explorer.bdv.BDVUtils; import net.preibisch.mvrecon.fiji.spimdata.explorer.popup.BDVPopup; import net.preibisch.mvrecon.fiji.spimdata.explorer.popup.ExplorerWindowSetable; import net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPoints; @@ -362,11 +362,16 @@ public static void resetBDVManualTransformations( BigDataViewer bdv ) return; // reset manual transform for all views - for ( int sourceIdx = 0; sourceIdx < bdv.getViewer().getVisibilityAndGrouping().getSources().size(); sourceIdx++ ) + final AffineTransform3D identity = new AffineTransform3D(); + final ViewerState state = bdv.getViewer().state(); + synchronized ( state ) { - SourceState< ? > s = bdv.getViewer().getVisibilityAndGrouping().getSources().get( sourceIdx ); - ( ( TransformedSource< ? > ) s.getSpimSource() ).setFixedTransform( new AffineTransform3D() ); - ( ( TransformedSource< ? > ) s.getSpimSource() ).setIncrementalTransform( new AffineTransform3D() ); + BDVUtils.forEachTransformedSource( + state.getSources(), + ( soc, source ) -> { + source.setFixedTransform( identity ); + source.setIncrementalTransform( identity ); + } ); } } @@ -383,9 +388,9 @@ public static void updateBDV( return; // we always set the fused mode - //setFusedModeSimple( bdv, data ); + setFusedModeSimple( bdv, data ); - //resetBDVManualTransformations( bdv ); + resetBDVManualTransformations( bdv ); if ( selectedRows == null || selectedRows.size() == 0 ) return; @@ -393,25 +398,35 @@ public static void updateBDV( if ( firstVD == null ) firstVD = selectedRows.iterator().next().get( 0 ); + final ViewerState state = bdv.getViewer().state(); + // always use the first timepoint final TimePoint firstTP = firstVD.getTimePoint(); - if ( bdv.getViewer().getState().getCurrentTimepoint() != getBDVTimePointIndex( firstTP, data ) ) - bdv.getViewer().setTimepoint( getBDVTimePointIndex( firstTP, data ) ); + state.setCurrentTimepoint( getBDVTimePointIndex( firstTP, data ) ); - final boolean[] active = new boolean[data.getSequenceDescription().getViewSetupsOrdered().size()]; + final Set< Integer > selectedViewSetupIds = selectedRows.stream() + .flatMap( Collection::stream ) + .filter( vd -> vd.getTimePointId() == firstTP.getId() ) + .map( ViewId::getViewSetupId ) + .collect( Collectors.toSet() ); - for ( final List< ? extends BasicViewDescription< ? > > vds : selectedRows ) - for ( BasicViewDescription< ? > vd : vds){ - if ( vd.getTimePointId() == firstTP.getId() ) - active[getBDVSourceIndex( vd.getViewSetup(), data )] = true; - } + final List< SourceAndConverter< ? > > active = new ArrayList<>(); + synchronized ( state ) + { + BDVUtils.forEachAbstractSpimSource( + state.getSources(), + ( soc, source ) -> { + if ( selectedViewSetupIds.contains( source.getSetupId() ) ) + active.add( soc ); + } ); + } + setVisibleSources( state, active ); // if ( selectedRows.size() > 1 && colorMode ) // colorSources( bdv.getSetupAssignments().getConverterSetups(), data, channelColors); // else // whiteSources( bdv.getSetupAssignments().getConverterSetups() ); - setVisibleSources( bdv.getViewer().getVisibilityAndGrouping(), active ); bdv.getViewer().requestRepaint(); } @@ -420,40 +435,33 @@ public static void setFusedModeSimple( final BigDataViewer bdv, final AbstractSp if ( bdv == null ) return; - if ( bdv.getViewer().getVisibilityAndGrouping().getDisplayMode() != DisplayMode.FUSED ) - { - final boolean[] active = new boolean[ data.getSequenceDescription().getViewSetupsOrdered().size() ]; - active[ 0 ] = true; - setVisibleSources( bdv.getViewer().getVisibilityAndGrouping(), active ); - bdv.getViewer().getVisibilityAndGrouping().setDisplayMode( DisplayMode.FUSED ); - } - } - - public static void colorSources( final List< ConverterSetup > cs, AbstractSpimData< ? > data, Map< Channel, ARGBType > channelColors ) - { - for ( int i = 0; i < cs.size(); ++i ) + final ViewerState state = bdv.getViewer().state(); + if ( state.getDisplayMode() != DisplayMode.FUSED ) { - Channel ch = data.getSequenceDescription().getViewSetups().get( cs.get( i ).getSetupId() ).getAttribute( Channel.class ); - cs.get( i ).setColor( channelColors.get( ch ) ); + setVisibleSources( state, state.getSources().subList( 0, 0 ) ); + state.setDisplayMode( DisplayMode.FUSED ); } } + // TODO (TP) This has duplicates in StitchingExplorerPanel and ViewSetupExplorerPanel + // Move to common utility class? public static void whiteSources( final List< ConverterSetup > cs ) { - for ( int i = 0; i < cs.size(); ++i ) - cs.get( i ).setColor( new ARGBType( ARGBType.rgba( 255, 255, 255, 255 ) ) ); + sameColorSources( cs, 255, 255, 255, 255 ); } public static void sameColorSources( final List< ConverterSetup > cs, final int r, final int g, final int b, final int a ) { - for ( int i = 0; i < cs.size(); ++i ) - cs.get( i ).setColor( new ARGBType( ARGBType.rgba( r, g, b, a ) ) ); + final ARGBType color = new ARGBType( ARGBType.rgba( r, g, b, a ) ); + cs.forEach( c -> c.setColor( color ) ); } - public static void setVisibleSources( final VisibilityAndGrouping vag, final boolean[] active ) + public static void setVisibleSources( final ViewerState state, final Collection< ? extends SourceAndConverter< ? > > active ) { - for ( int i = 0; i < active.length; ++i ) - vag.setSourceActive( i, active[ i ] ); + final List< SourceAndConverter< ? > > inactive = new ArrayList<>( state.getSources() ); + inactive.removeAll( active ); + state.setSourcesActive( inactive, false ); + state.setSourcesActive( active, true ); } public static int getBDVTimePointIndex( final TimePoint t, final AbstractSpimData< ? > data ) diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/bdv/BDVUtils.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/bdv/BDVUtils.java new file mode 100644 index 000000000..a9d61dc8c --- /dev/null +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/bdv/BDVUtils.java @@ -0,0 +1,40 @@ +package net.preibisch.mvrecon.fiji.spimdata.explorer.bdv; + +import bdv.AbstractSpimSource; +import bdv.tools.transformation.TransformedSource; +import bdv.viewer.Source; +import bdv.viewer.SourceAndConverter; +import java.util.Collection; +import java.util.function.BiConsumer; + +public class BDVUtils +{ + public static void forEachAbstractSpimSource( + final Collection< ? extends SourceAndConverter< ? > > sources, + final BiConsumer< ? super SourceAndConverter< ? >, ? super AbstractSpimSource< ? > > action ) + { + for ( final SourceAndConverter< ? > soc : sources ) + { + Source< ? > source = soc.getSpimSource(); + + if ( source instanceof TransformedSource ) + source = ( ( TransformedSource< ? > ) source ).getWrappedSource(); + + if ( source instanceof AbstractSpimSource ) + action.accept( soc, ( AbstractSpimSource< ? > ) source ); + } + } + + public static void forEachTransformedSource( + final Collection< ? extends SourceAndConverter< ? > > sources, + final BiConsumer< ? super SourceAndConverter< ? >, ? super TransformedSource< ? > > action ) + { + for ( final SourceAndConverter< ? > soc : sources ) + { + Source< ? > source = soc.getSpimSource(); + + if ( source instanceof TransformedSource ) + action.accept( soc, ( TransformedSource< ? > ) source ); + } + } +} From fa3a2dbd1d482db3e925c402105c054912337569 Mon Sep 17 00:00:00 2001 From: Stephan Preibisch Date: Thu, 16 Nov 2023 10:11:51 -0500 Subject: [PATCH 11/13] start fixing Messages in BigStitcher (TODO: checkbox "do not show BDV") --- .../queryXML/GenericLoadParseQueryXML.java | 2 +- .../mvrecon/fiji/plugin/util/GUIHelper.java | 16 ++++++++-------- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/queryXML/GenericLoadParseQueryXML.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/queryXML/GenericLoadParseQueryXML.java index 1df5ec501..69eda5c41 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/plugin/queryXML/GenericLoadParseQueryXML.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/plugin/queryXML/GenericLoadParseQueryXML.java @@ -316,7 +316,7 @@ public boolean queryXML( this.gd = gd; gd.addMessage( "" ); - GUIHelper.addPreibischLabWebsite( gd ); + GUIHelper.addCredits( gd ); gd.showDialog(); diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/util/GUIHelper.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/util/GUIHelper.java index 25c404609..55727aa52 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/plugin/util/GUIHelper.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/plugin/util/GUIHelper.java @@ -73,13 +73,13 @@ public class GUIHelper public static Font staticfont = new Font( Font.MONOSPACED, Font.PLAIN, 12 ); - final public static String myURL = "http://preibischlab.mdc-berlin.de/"; - final public static String paperURL = "http://www.nature.com/nmeth/journal/v7/n6/full/nmeth0610-418.html"; - final public static String messagePaper = "Please note that the SPIM Registration is based on a publication.\n" + + final public static String myURL = "https://www.janelia.org/open-science/overview/open-science-software-initiative-ossi"; + final public static String paperURL = "https://www.nature.com/articles/s41592-019-0501-0"; + final public static String messagePaper = "Please note that BigStitcher is based on a publication.\n" + "If you use it successfully for your research please be so kind to cite our work:\n" + - "Preibisch et al., Nature Methods (2010), 7(6):418-419\n"; + "Nature Methods 16: 870–874 (2019)\n"; - final public static String messageWebsite = "This plugin is written and maintained by the Preibisch Lab (click for webpage)\n"; + final public static String messageWebsite = "This plugin was written by the Preibisch Lab is now supported by the HHMI Janelia Open Science Software initative\n"; public static void addNatMethBeadsPaper( final GenericDialog gd ) { addNatMethBeadsPaper( gd, messagePaper ); } public static void addNatMethBeadsPaper( final GenericDialog gd, final String msg ) { addHyperLink( gd, msg, paperURL ); } @@ -94,11 +94,11 @@ public static final void addHyperLink( final GenericDialog gd, final String msg, GUIHelper.addHyperLinkListener( text, url ); } - public static final void addPreibischLabWebsite( final GenericDialog gd ) + public static final void addCredits( final GenericDialog gd ) { - gd.addMessage( "This software is developed by the Preibisch Lab in collaboration with the ImgLib2 and Fiji team\nhttp://preibischlab.mdc-berlin.de/", new Font( Font.SANS_SERIF, Font.BOLD, 12 ) ); + gd.addMessage( "This software was developed by the Preibisch Lab (MDC Berlin) and is now supported by the\nHHMI Janelia Open Science Software initative in collaboration with the ImgLib2 and Fiji team", new Font( Font.SANS_SERIF, Font.BOLD, 12 ) ); MultiLineLabel text = (MultiLineLabel) gd.getMessage(); - GUIHelper.addHyperLinkListener( text, "http://preibischlab.github.io/preibisch-labsite" ); + GUIHelper.addHyperLinkListener( text, "https://www.janelia.org/open-science/overview/open-science-software-initiative-ossi" ); } public static void displayRegistrationNames( final GenericDialog gd, final HashMap< String, Integer > names ) From 90e1bb2309ec185c0149d491845b32e3c20be0b1 Mon Sep 17 00:00:00 2001 From: Stephan Preibisch Date: Thu, 16 Nov 2023 10:31:13 -0500 Subject: [PATCH 12/13] uodate license headers --- .../fiji/spimdata/explorer/bdv/BDVUtils.java | 22 +++++++++++++++++++ .../spimdata/explorer/popup/BDVPopup.java | 4 ++-- 2 files changed, 24 insertions(+), 2 deletions(-) diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/bdv/BDVUtils.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/bdv/BDVUtils.java index a9d61dc8c..8046a2351 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/bdv/BDVUtils.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/bdv/BDVUtils.java @@ -1,3 +1,25 @@ +/*- + * #%L + * Software for the reconstruction of multi-view microscopic acquisitions + * like Selective Plane Illumination Microscopy (SPIM) Data. + * %% + * Copyright (C) 2012 - 2023 Multiview Reconstruction developers. + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 2 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * . + * #L% + */ package net.preibisch.mvrecon.fiji.spimdata.explorer.bdv; import bdv.AbstractSpimSource; diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java index 5ecdffa8f..0c92b2e06 100644 --- a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java +++ b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/BDVPopup.java @@ -9,12 +9,12 @@ * it under the terms of the GNU General Public License as * published by the Free Software Foundation, either version 2 of the * License, or (at your option) any later version. - * + * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. - * + * * You should have received a copy of the GNU General Public * License along with this program. If not, see * . From cbc2ce3ec2b4a64d5fb83b7f9fa88fb7889a55c9 Mon Sep 17 00:00:00 2001 From: Stephan Preibisch Date: Thu, 16 Nov 2023 10:32:45 -0500 Subject: [PATCH 13/13] Bump to next development cycle Signed-off-by: Stephan Preibisch --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index 800983e01..c02b14589 100644 --- a/pom.xml +++ b/pom.xml @@ -11,7 +11,7 @@ net.preibisch multiview-reconstruction - 3.2.5-SNAPSHOT + 3.2.6-SNAPSHOT Multiview Reconstruction Software for the reconstruction of multi-view microscopic acquisitions