diff --git a/src/main/java/bdv/ij/BigDataBrowserPlugIn.java b/src/main/java/bdv/ij/BigDataBrowserPlugIn.java
index c1102e55177aac812801e8bd35084ae9ca26be3d..6907f3c46548f5f81a60cd64a1e8700ffacf0593 100644
--- a/src/main/java/bdv/ij/BigDataBrowserPlugIn.java
+++ b/src/main/java/bdv/ij/BigDataBrowserPlugIn.java
@@ -1,15 +1,12 @@
package bdv.ij;
-import ij.IJ;
-import ij.ImageJ;
-import ij.plugin.PlugIn;
-
import java.awt.Component;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.image.BufferedImage;
+import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
@@ -27,23 +24,26 @@ import javax.swing.JList;
import javax.swing.JOptionPane;
import javax.swing.JScrollPane;
-import mpicbg.spim.data.SpimDataException;
-
import org.apache.commons.lang.StringUtils;
+import com.google.gson.stream.JsonReader;
+
import bdv.BigDataViewer;
import bdv.ij.util.ProgressWriterIJ;
-
-import com.google.gson.stream.JsonReader;
+import bdv.viewer.ViewerOptions;
+import ij.IJ;
+import ij.ImageJ;
+import ij.plugin.PlugIn;
+import mpicbg.spim.data.SpimDataException;
/**
* @author HongKee Moon <moon@mpi-cbg.de>
*/
public class BigDataBrowserPlugIn implements PlugIn
{
- private final Map< String, ImageIcon > imageMap = new HashMap< String, ImageIcon >();
+ private final Map< String, ImageIcon > imageMap = new HashMap<>();
- private final Map< String, String > datasetUrlMap = new HashMap< String, String >();
+ private final Map< String, String > datasetUrlMap = new HashMap<>();
public static String serverUrl = "http://";
@@ -68,7 +68,7 @@ public class BigDataBrowserPlugIn implements PlugIn
serverUrl = remoteUrl.toString();
- final ArrayList< String > nameList = new ArrayList< String >();
+ final ArrayList< String > nameList = new ArrayList<>();
try
{
getDatasetList( serverUrl, nameList );
diff --git a/src/main/java/bdv/ij/ExportImagePlusPlugIn.java b/src/main/java/bdv/ij/ExportImagePlusPlugIn.java
index 5300891c06769dc56c8165294ccd985113091050..38935e9b528c74a2671b9c8fe4453ba5d6234aa9 100644
--- a/src/main/java/bdv/ij/ExportImagePlusPlugIn.java
+++ b/src/main/java/bdv/ij/ExportImagePlusPlugIn.java
@@ -1,14 +1,5 @@
package bdv.ij;
-import fiji.util.gui.GenericDialogPlus;
-import ij.IJ;
-import ij.ImageJ;
-import ij.ImagePlus;
-import ij.WindowManager;
-import ij.gui.DialogListener;
-import ij.gui.GenericDialog;
-import ij.plugin.PlugIn;
-
import java.awt.AWTEvent;
import java.awt.Checkbox;
import java.awt.Choice;
@@ -19,16 +10,6 @@ import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
-import mpicbg.spim.data.generic.sequence.BasicViewSetup;
-import mpicbg.spim.data.registration.ViewRegistration;
-import mpicbg.spim.data.registration.ViewRegistrations;
-import mpicbg.spim.data.sequence.Channel;
-import mpicbg.spim.data.sequence.FinalVoxelDimensions;
-import mpicbg.spim.data.sequence.TimePoint;
-import mpicbg.spim.data.sequence.TimePoints;
-import net.imglib2.FinalDimensions;
-import net.imglib2.RandomAccessibleInterval;
-import net.imglib2.realtransform.AffineTransform3D;
import bdv.export.ExportMipmapInfo;
import bdv.export.ProgressWriter;
import bdv.export.ProposeMipmaps;
@@ -45,6 +26,24 @@ import bdv.img.hdf5.Partition;
import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal;
+import fiji.util.gui.GenericDialogPlus;
+import ij.IJ;
+import ij.ImageJ;
+import ij.ImagePlus;
+import ij.WindowManager;
+import ij.gui.DialogListener;
+import ij.gui.GenericDialog;
+import ij.plugin.PlugIn;
+import mpicbg.spim.data.generic.sequence.BasicViewSetup;
+import mpicbg.spim.data.registration.ViewRegistration;
+import mpicbg.spim.data.registration.ViewRegistrations;
+import mpicbg.spim.data.sequence.Channel;
+import mpicbg.spim.data.sequence.FinalVoxelDimensions;
+import mpicbg.spim.data.sequence.TimePoint;
+import mpicbg.spim.data.sequence.TimePoints;
+import net.imglib2.FinalDimensions;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.realtransform.AffineTransform3D;
/**
* ImageJ plugin to export the current image to xml/hdf5.
@@ -140,20 +139,20 @@ public class ExportImagePlusPlugIn implements PlugIn
sourceTransform.set( pw, 0, 0, 0, 0, ph, 0, 0, 0, 0, pd, 0 );
// write hdf5
- final HashMap< Integer, BasicViewSetup > setups = new HashMap< Integer, BasicViewSetup >( numSetups );
+ final HashMap< Integer, BasicViewSetup > setups = new HashMap<>( numSetups );
for ( int s = 0; s < numSetups; ++s )
{
final BasicViewSetup setup = new BasicViewSetup( s, String.format( "channel %d", s + 1 ), size, voxelSize );
setup.setAttribute( new Channel( s + 1 ) );
setups.put( s, setup );
}
- final ArrayList< TimePoint > timepoints = new ArrayList< TimePoint >( numTimepoints );
+ final ArrayList< TimePoint > timepoints = new ArrayList<>( numTimepoints );
for ( int t = 0; t < numTimepoints; ++t )
timepoints.add( new TimePoint( t ) );
final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal( new TimePoints( timepoints ), setups, imgLoader, null );
Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo;
- perSetupExportMipmapInfo = new HashMap< Integer, ExportMipmapInfo >();
+ perSetupExportMipmapInfo = new HashMap<>();
final ExportMipmapInfo mipmapInfo = new ExportMipmapInfo( params.resolutions, params.subdivisions );
for ( final BasicViewSetup setup : seq.getViewSetupsOrdered() )
perSetupExportMipmapInfo.put( setup.getId(), mipmapInfo );
@@ -235,7 +234,7 @@ public class ExportImagePlusPlugIn implements PlugIn
final Hdf5ImageLoader hdf5Loader = new Hdf5ImageLoader( params.hdf5File, partitions, null, false );
final SequenceDescriptionMinimal seqh5 = new SequenceDescriptionMinimal( seq, hdf5Loader );
- final ArrayList< ViewRegistration > registrations = new ArrayList< ViewRegistration >();
+ final ArrayList< ViewRegistration > registrations = new ArrayList<>();
for ( int t = 0; t < numTimepoints; ++t )
for ( int s = 0; s < numSetups; ++s )
registrations.add( new ViewRegistration( t, s, sourceTransform ) );
diff --git a/src/main/java/bdv/ij/ExportSpimFusionPlugIn.java b/src/main/java/bdv/ij/ExportSpimFusionPlugIn.java
index ac005f0722a6824377d164cdaf376b88f212cabe..742f2588181214b68006b2d316de81bcbab16102 100644
--- a/src/main/java/bdv/ij/ExportSpimFusionPlugIn.java
+++ b/src/main/java/bdv/ij/ExportSpimFusionPlugIn.java
@@ -1,14 +1,5 @@
package bdv.ij;
-import fiji.plugin.Bead_Registration;
-import fiji.plugin.Multi_View_Fusion;
-import fiji.util.gui.GenericDialogPlus;
-import ij.IJ;
-import ij.ImagePlus;
-import ij.gui.DialogListener;
-import ij.gui.GenericDialog;
-import ij.plugin.PlugIn;
-
import java.awt.AWTEvent;
import java.awt.Checkbox;
import java.awt.TextField;
@@ -26,6 +17,31 @@ import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import bdv.export.ExportMipmapInfo;
+import bdv.export.ProgressWriter;
+import bdv.export.ProposeMipmaps;
+import bdv.export.SubTaskProgressWriter;
+import bdv.export.WriteSequenceToHdf5;
+import bdv.ij.export.FusionResult;
+import bdv.ij.export.SpimRegistrationSequence;
+import bdv.ij.export.ViewSetupWrapper;
+import bdv.ij.util.PluginHelper;
+import bdv.ij.util.ProgressWriterIJ;
+import bdv.img.hdf5.Hdf5ImageLoader;
+import bdv.img.hdf5.MipmapInfo;
+import bdv.img.hdf5.Partition;
+import bdv.img.hdf5.Util;
+import bdv.spimdata.SequenceDescriptionMinimal;
+import bdv.spimdata.SpimDataMinimal;
+import bdv.spimdata.XmlIoSpimDataMinimal;
+import fiji.plugin.Bead_Registration;
+import fiji.plugin.Multi_View_Fusion;
+import fiji.util.gui.GenericDialogPlus;
+import ij.IJ;
+import ij.ImagePlus;
+import ij.gui.DialogListener;
+import ij.gui.GenericDialog;
+import ij.plugin.PlugIn;
import mpicbg.spim.data.SpimDataException;
import mpicbg.spim.data.generic.sequence.BasicImgLoader;
import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
@@ -48,23 +64,6 @@ import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.util.Pair;
import net.imglib2.util.ValuePair;
import spimopener.SPIMExperiment;
-import bdv.export.ExportMipmapInfo;
-import bdv.export.ProgressWriter;
-import bdv.export.ProposeMipmaps;
-import bdv.export.SubTaskProgressWriter;
-import bdv.export.WriteSequenceToHdf5;
-import bdv.ij.export.FusionResult;
-import bdv.ij.export.SpimRegistrationSequence;
-import bdv.ij.export.ViewSetupWrapper;
-import bdv.ij.util.PluginHelper;
-import bdv.ij.util.ProgressWriterIJ;
-import bdv.img.hdf5.Hdf5ImageLoader;
-import bdv.img.hdf5.MipmapInfo;
-import bdv.img.hdf5.Partition;
-import bdv.img.hdf5.Util;
-import bdv.spimdata.SequenceDescriptionMinimal;
-import bdv.spimdata.SpimDataMinimal;
-import bdv.spimdata.XmlIoSpimDataMinimal;
public class ExportSpimFusionPlugIn implements PlugIn
{
@@ -137,27 +136,27 @@ public class ExportSpimFusionPlugIn implements PlugIn
final Hdf5ImageLoader existingHdf5Loader = ( Hdf5ImageLoader ) existingSequence.getImgLoader();
// maps every existing timepoint id to itself, needed for partitions
- final Map< Integer, Integer > timepointIdentityMap = new HashMap< Integer, Integer >();
+ final Map< Integer, Integer > timepointIdentityMap = new HashMap<>();
for ( final TimePoint tp : existingSequence.getTimePoints().getTimePointsOrdered() )
timepointIdentityMap.put( tp.getId(), tp.getId() );
// maps every existing setup id to itself, needed for partitions
- final Map< Integer, Integer > setupIdentityMap = new HashMap< Integer, Integer >();
+ final Map< Integer, Integer > setupIdentityMap = new HashMap<>();
for ( final int s : existingSequence.getViewSetups().keySet() )
setupIdentityMap.put( s, s );
// create partition list for existing dataset
- final ArrayList< Partition > partitions = new ArrayList< Partition >( existingHdf5Loader.getPartitions() );
+ final ArrayList< Partition > partitions = new ArrayList<>( existingHdf5Loader.getPartitions() );
final boolean notYetPartitioned = partitions.isEmpty();
if ( notYetPartitioned )
// add one partition for the unpartitioned existing dataset
partitions.add( new Partition( existingHdf5Loader.getHdf5File().getAbsolutePath(), timepointIdentityMap, setupIdentityMap ) );
// wrap fused data setups with unused setup ids
- final HashSet< Integer > usedSetupIds = new HashSet< Integer >( existingSequence.getViewSetups().keySet() );
- final HashMap< Integer, ViewSetupWrapper > fusionSetups = new HashMap< Integer, ViewSetupWrapper >();
- final HashMap< Integer, BasicSetupImgLoader< ? > > fusionSetupImgLoaders = new HashMap< Integer, BasicSetupImgLoader< ? > >();
- final ArrayList< ViewRegistration > fusionRegistrations = new ArrayList< ViewRegistration >();
+ final HashSet< Integer > usedSetupIds = new HashSet<>( existingSequence.getViewSetups().keySet() );
+ final HashMap< Integer, ViewSetupWrapper > fusionSetups = new HashMap<>();
+ final HashMap< Integer, BasicSetupImgLoader< ? > > fusionSetupImgLoaders = new HashMap<>();
+ final ArrayList< ViewRegistration > fusionRegistrations = new ArrayList<>();
for ( final BasicViewSetup s : fusionSeq.getViewSetupsOrdered() )
{
int fusionSetupId = 0;
@@ -190,7 +189,7 @@ public class ExportSpimFusionPlugIn implements PlugIn
fusionReg = new ViewRegistrations( fusionRegistrations );
// add partitions for the fused data and split if desired
- final ArrayList< Partition > newPartitions = new ArrayList< Partition >();
+ final ArrayList< Partition > newPartitions = new ArrayList<>();
final String xmlFilename = params.seqFile.getAbsolutePath();
final String basename = xmlFilename.endsWith( ".xml" ) ? xmlFilename.substring( 0, xmlFilename.length() - 4 ) : xmlFilename;
if ( params.split )
@@ -209,7 +208,7 @@ public class ExportSpimFusionPlugIn implements PlugIn
else
{
final String path = PluginHelper.createNewPartitionFile( basename ).getAbsolutePath();
- final HashMap< Integer, Integer > setupIdSequenceToPartition = new HashMap< Integer, Integer >();
+ final HashMap< Integer, Integer > setupIdSequenceToPartition = new HashMap<>();
for ( final BasicViewSetup s : fusionSeq.getViewSetupsOrdered() )
setupIdSequenceToPartition.put( s.getId(), s.getId() );
final Partition partition = new Partition( path, timepointIdentityMap, setupIdSequenceToPartition );
@@ -218,7 +217,7 @@ public class ExportSpimFusionPlugIn implements PlugIn
}
// create ExportMipmapInfos for the fused data setups
- final Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo = new HashMap< Integer, ExportMipmapInfo >();
+ final Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo = new HashMap<>();
final ExportMipmapInfo mipmapInfo = new ExportMipmapInfo( params.resolutions, params.subdivisions );
for ( final BasicViewSetup setup : fusionSeq.getViewSetupsOrdered() )
perSetupExportMipmapInfo.put( setup.getId(), mipmapInfo );
@@ -240,7 +239,7 @@ public class ExportSpimFusionPlugIn implements PlugIn
// TODO: For now the timepoints are just taken from the fusionSeq.
// To do it properly, timepoints from existing dataset and fusionSeq should be combined.
final TimePoints aggregateTimePoints = fusionSeq.getTimePoints();
- final HashMap< Integer, BasicViewSetup > aggregateSetups = new HashMap< Integer, BasicViewSetup >();
+ final HashMap< Integer, BasicViewSetup > aggregateSetups = new HashMap<>();
for ( final BasicViewSetup s : existingSequence.getViewSetupsOrdered() )
aggregateSetups.put( s.getId(), s );
for ( final BasicViewSetup s : fusionSeq.getViewSetupsOrdered() )
@@ -256,7 +255,7 @@ public class ExportSpimFusionPlugIn implements PlugIn
aggregateMissingViews );
// create aggregate ExportMipmapInfos
- final HashMap< Integer, ExportMipmapInfo > aggregateMipmapInfos = new HashMap< Integer, ExportMipmapInfo >( perSetupExportMipmapInfo );
+ final HashMap< Integer, ExportMipmapInfo > aggregateMipmapInfos = new HashMap<>( perSetupExportMipmapInfo );
for ( final BasicViewSetup s : existingSequence.getViewSetupsOrdered() )
{
final MipmapInfo info = existingHdf5Loader.getSetupImgLoader( s.getId() ).getMipmapInfo();
@@ -266,7 +265,7 @@ public class ExportSpimFusionPlugIn implements PlugIn
}
// create aggregate ViewRegistrations
- final ArrayList< ViewRegistration > regs = new ArrayList< ViewRegistration >();
+ final ArrayList< ViewRegistration > regs = new ArrayList<>();
regs.addAll( existingSpimData.getViewRegistrations().getViewRegistrationsOrdered() );
regs.addAll( fusionReg.getViewRegistrationsOrdered() );
final ViewRegistrations aggregateViewRegistrstions = new ViewRegistrations( regs );
@@ -312,7 +311,7 @@ public class ExportSpimFusionPlugIn implements PlugIn
final SequenceDescriptionMinimal desc = fusionResult.getSequenceDescription();
// create ExportMipmapInfos
- final Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo = new HashMap< Integer, ExportMipmapInfo >();
+ final Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo = new HashMap<>();
final ExportMipmapInfo mipmapInfo = new ExportMipmapInfo( params.resolutions, params.subdivisions );
for ( final BasicViewSetup setup : desc.getViewSetupsOrdered() )
perSetupExportMipmapInfo.put( setup.getId(), mipmapInfo );
@@ -571,7 +570,7 @@ public class ExportSpimFusionPlugIn implements PlugIn
else
{
numChannels = 1;
- channels = new ArrayList<Integer>();
+ channels = new ArrayList<>();
channels.add( 0 );
}
@@ -614,7 +613,7 @@ public class ExportSpimFusionPlugIn implements PlugIn
// test which registration files are there for each channel
// file = new File[ timepoints.length ][ channels.length ][ angles.length ];
- final ArrayList<ArrayList<Integer>> timepoints = new ArrayList<ArrayList<Integer>>();
+ final ArrayList<ArrayList<Integer>> timepoints = new ArrayList<>();
int numChoices = 0;
conf.zStretching = -1;
@@ -987,7 +986,7 @@ public class ExportSpimFusionPlugIn implements PlugIn
final Pair< String, Integer > pair = detectPatternAndNumSlices( subdir, someTimepoint );
if ( pair == null )
return null;
- return new ValuePair< String, Integer >( "%1$d/" + pair.getA(), pair.getB() );
+ return new ValuePair<>( "%1$d/" + pair.getA(), pair.getB() );
}
String zeros = "";
@@ -1028,7 +1027,7 @@ public class ExportSpimFusionPlugIn implements PlugIn
final int numSlices = files2.length;
IOFunctions.println( "detected numSlices = " + numSlices );
- return new ValuePair< String, Integer >( pattern, new Integer( numSlices ) );
+ return new ValuePair<>( pattern, new Integer( numSlices ) );
}
}
return null;
diff --git a/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java b/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java
index 0ccf6c7574d35d30d02ef3043fbb69c7d57bc17f..39b70b0bbcee418e1a144f448f142c7dce507ffb 100644
--- a/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java
+++ b/src/main/java/bdv/ij/ExportSpimSequencePlugIn.java
@@ -1,13 +1,5 @@
package bdv.ij;
-import fiji.plugin.Bead_Registration;
-import fiji.plugin.Multi_View_Fusion;
-import fiji.util.gui.GenericDialogPlus;
-import ij.IJ;
-import ij.gui.DialogListener;
-import ij.gui.GenericDialog;
-import ij.plugin.PlugIn;
-
import java.awt.AWTEvent;
import java.awt.Checkbox;
import java.awt.TextField;
@@ -23,13 +15,6 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import mpicbg.spim.data.generic.sequence.BasicViewSetup;
-import mpicbg.spim.data.sequence.TimePoint;
-import mpicbg.spim.io.ConfigurationParserException;
-import mpicbg.spim.io.IOFunctions;
-import mpicbg.spim.io.SPIMConfiguration;
-import mpicbg.spim.io.TextFileAccess;
-import spimopener.SPIMExperiment;
import bdv.export.ExportMipmapInfo;
import bdv.export.ProgressWriter;
import bdv.export.ProposeMipmaps;
@@ -43,6 +28,20 @@ import bdv.img.hdf5.Partition;
import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal;
+import fiji.plugin.Bead_Registration;
+import fiji.plugin.Multi_View_Fusion;
+import fiji.util.gui.GenericDialogPlus;
+import ij.IJ;
+import ij.gui.DialogListener;
+import ij.gui.GenericDialog;
+import ij.plugin.PlugIn;
+import mpicbg.spim.data.generic.sequence.BasicViewSetup;
+import mpicbg.spim.data.sequence.TimePoint;
+import mpicbg.spim.io.ConfigurationParserException;
+import mpicbg.spim.io.IOFunctions;
+import mpicbg.spim.io.SPIMConfiguration;
+import mpicbg.spim.io.TextFileAccess;
+import spimopener.SPIMExperiment;
public class ExportSpimSequencePlugIn implements PlugIn
{
@@ -63,7 +62,7 @@ public class ExportSpimSequencePlugIn implements PlugIn
Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo;
if ( params.setMipmapManual )
{
- perSetupExportMipmapInfo = new HashMap< Integer, ExportMipmapInfo >();
+ perSetupExportMipmapInfo = new HashMap<>();
final ExportMipmapInfo mipmapInfo = new ExportMipmapInfo( params.resolutions, params.subdivisions );
for ( final BasicViewSetup setup : desc.getViewSetupsOrdered() )
perSetupExportMipmapInfo.put( setup.getId(), mipmapInfo );
@@ -327,7 +326,7 @@ public class ExportSpimSequencePlugIn implements PlugIn
else
{
numChannels = 1;
- channels = new ArrayList< Integer >();
+ channels = new ArrayList<>();
channels.add( 0 );
}
@@ -372,7 +371,7 @@ public class ExportSpimSequencePlugIn implements PlugIn
// test which registration files are there for each channel
// file = new File[ timepoints.length ][ channels.length ][
// angles.length ];
- final ArrayList< ArrayList< Integer >> timepoints = new ArrayList< ArrayList< Integer >>();
+ final ArrayList< ArrayList< Integer > > timepoints = new ArrayList<>();
int numChoices = 0;
conf.zStretching = -1;
diff --git a/src/main/java/bdv/ij/OpenImagePlusPlugIn.java b/src/main/java/bdv/ij/OpenImagePlusPlugIn.java
index 71608a49143c5c52482bb1191b00ec7f6159de00..9110df3527da5fa531172e4ae11ed70f3674bbb2 100644
--- a/src/main/java/bdv/ij/OpenImagePlusPlugIn.java
+++ b/src/main/java/bdv/ij/OpenImagePlusPlugIn.java
@@ -148,7 +148,7 @@ public class OpenImagePlusPlugIn implements PlugIn
final int numSetups = imp.getNChannels();
// create setups from channels
- final HashMap< Integer, BasicViewSetup > setups = new HashMap< Integer, BasicViewSetup >( numSetups );
+ final HashMap< Integer, BasicViewSetup > setups = new HashMap<>( numSetups );
for ( int s = 0; s < numSetups; ++s )
{
final BasicViewSetup setup = new BasicViewSetup( s, String.format( "channel %d", s + 1 ), size, voxelSize );
@@ -157,7 +157,7 @@ public class OpenImagePlusPlugIn implements PlugIn
}
// create timepoints
- final ArrayList< TimePoint > timepoints = new ArrayList< TimePoint >( numTimepoints );
+ final ArrayList< TimePoint > timepoints = new ArrayList<>( numTimepoints );
for ( int t = 0; t < numTimepoints; ++t )
timepoints.add( new TimePoint( t ) );
final SequenceDescriptionMinimal seq = new SequenceDescriptionMinimal( new TimePoints( timepoints ), setups, imgLoader, null );
@@ -165,7 +165,7 @@ public class OpenImagePlusPlugIn implements PlugIn
// create ViewRegistrations from the images calibration
final AffineTransform3D sourceTransform = new AffineTransform3D();
sourceTransform.set( pw, 0, 0, 0, 0, ph, 0, 0, 0, 0, pd, 0 );
- final ArrayList< ViewRegistration > registrations = new ArrayList< ViewRegistration >();
+ final ArrayList< ViewRegistration > registrations = new ArrayList<>();
for ( int t = 0; t < numTimepoints; ++t )
for ( int s = 0; s < numSetups; ++s )
registrations.add( new ViewRegistration( t, s, sourceTransform ) );
diff --git a/src/main/java/bdv/ij/export/FixAbsolutePathsInHdf5Partitions.java b/src/main/java/bdv/ij/export/FixAbsolutePathsInHdf5Partitions.java
index a671318f17d1c670eaabcb432f544368d3b12f78..ac4e3d4a77771c4fc5b61fe96e626a984061ae29 100644
--- a/src/main/java/bdv/ij/export/FixAbsolutePathsInHdf5Partitions.java
+++ b/src/main/java/bdv/ij/export/FixAbsolutePathsInHdf5Partitions.java
@@ -5,8 +5,6 @@ import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
-import mpicbg.spim.data.SpimDataException;
-import mpicbg.spim.data.generic.sequence.BasicViewSetup;
import bdv.export.ExportMipmapInfo;
import bdv.export.WriteSequenceToHdf5;
import bdv.img.hdf5.Hdf5ImageLoader;
@@ -16,6 +14,8 @@ import bdv.img.hdf5.Util;
import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal;
+import mpicbg.spim.data.SpimDataException;
+import mpicbg.spim.data.generic.sequence.BasicViewSetup;
/**
* Older versions of multi-partition hdf5 export had a bug that caused absolute
@@ -38,7 +38,7 @@ public class FixAbsolutePathsInHdf5Partitions
final SequenceDescriptionMinimal seq = spimData.getSequenceDescription();
final Hdf5ImageLoader il = ( Hdf5ImageLoader) seq.getImgLoader();
final String outfn = il.getHdf5File().getCanonicalPath() + "FIXED";
- final HashMap< Integer, ExportMipmapInfo > perSetupMipmapInfo = new HashMap< Integer, ExportMipmapInfo >();
+ final HashMap< Integer, ExportMipmapInfo > perSetupMipmapInfo = new HashMap<>();
for ( final BasicViewSetup setup : seq.getViewSetupsOrdered() )
{
final int setupId = setup.getId();
diff --git a/src/main/java/bdv/ij/export/FusionResult.java b/src/main/java/bdv/ij/export/FusionResult.java
index 5475db5bef1ee388b4a3f91b6bd714f1aa207ae1..1a57fa72e76961a78342b424ed1ffd7cac0895a1 100644
--- a/src/main/java/bdv/ij/export/FusionResult.java
+++ b/src/main/java/bdv/ij/export/FusionResult.java
@@ -6,6 +6,8 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import bdv.ij.export.imgloader.FusionImageLoader;
+import bdv.spimdata.SequenceDescriptionMinimal;
import mpicbg.spim.data.generic.base.Entity;
import mpicbg.spim.data.generic.sequence.BasicViewSetup;
import mpicbg.spim.data.registration.ViewRegistration;
@@ -17,9 +19,6 @@ import mpicbg.spim.data.sequence.TimePoints;
import mpicbg.spim.data.sequence.VoxelDimensions;
import net.imglib2.Dimensions;
import net.imglib2.realtransform.AffineTransform3D;
-import net.imglib2.type.numeric.real.FloatType;
-import bdv.ij.export.imgloader.FusionImageLoader;
-import bdv.spimdata.SequenceDescriptionMinimal;
public class FusionResult
{
@@ -37,7 +36,7 @@ public class FusionResult
final Map< Integer, AffineTransform3D > perTimePointFusionTransforms )
{
// add one fused ViewSetup per channel in the SpimRegistrationSequence
- final List< Integer > channels = new ArrayList< Integer >();
+ final List< Integer > channels = new ArrayList<>();
for ( final BasicViewSetup setup : spimseq.getSequenceDescription().getViewSetupsOrdered() )
{
final int channel = setup.getAttribute( Channel.class ).getId();
@@ -57,9 +56,9 @@ public class FusionResult
final double sliceValueMax,
final Map< Integer, AffineTransform3D > perTimePointFusionTransforms )
{
- final HashMap< Integer, Integer > setupIdToChannelId = new HashMap< Integer, Integer >();
+ final HashMap< Integer, Integer > setupIdToChannelId = new HashMap<>();
setupIdToChannelId.put( 0, 0 );
- final ImgLoader fusionLoader = new FusionImageLoader< FloatType >( filepath +"/" + filepattern, setupIdToChannelId, numSlices, new FusionImageLoader.Gray32ImagePlusLoader(), sliceValueMin, sliceValueMax );
+ final ImgLoader fusionLoader = new FusionImageLoader<>( filepath +"/" + filepattern, setupIdToChannelId, numSlices, new FusionImageLoader.Gray32ImagePlusLoader(), sliceValueMin, sliceValueMax );
final int setupId = 0;
final String name = "fused";
final int timepointId = timepoints.getTimePointsOrdered().get( 0 ).getId();
@@ -67,7 +66,7 @@ public class FusionResult
final VoxelDimensions voxelSize = fusionLoader.getSetupImgLoader( setupId ).getVoxelSize( timepointId );
final BasicViewSetup setup = new BasicViewSetup( setupId, name, size, voxelSize );
desc = new SequenceDescriptionMinimal( timepoints, Entity.idMap( Arrays.asList( setup ) ), fusionLoader, null );
- final ArrayList< ViewRegistration > registrations = new ArrayList< ViewRegistration >();
+ final ArrayList< ViewRegistration > registrations = new ArrayList<>();
for ( final TimePoint timepoint : timepoints.getTimePointsOrdered() )
registrations.add( new ViewRegistration( timepoint.getId(), 0, perTimePointFusionTransforms.get( timepoint.getId() ) ) );
regs = new ViewRegistrations( registrations );
@@ -83,13 +82,13 @@ public class FusionResult
final double sliceValueMax,
final Map< Integer, AffineTransform3D > perTimePointFusionTransforms )
{
- final HashMap< Integer, Integer > setupIdToChannelId = new HashMap< Integer, Integer >();
+ final HashMap< Integer, Integer > setupIdToChannelId = new HashMap<>();
for ( int setupId = 0; setupId < channels.size(); ++setupId )
{
setupIdToChannelId.put( setupId, channels.get( setupId ) );
}
- final ImgLoader fusionLoader = new FusionImageLoader< FloatType >( filepath +"/" + filepattern, setupIdToChannelId, numSlices, new FusionImageLoader.Gray32ImagePlusLoader(), sliceValueMin, sliceValueMax );
- final ArrayList< BasicViewSetup > setups = new ArrayList< BasicViewSetup >();
+ final ImgLoader fusionLoader = new FusionImageLoader<>( filepath +"/" + filepattern, setupIdToChannelId, numSlices, new FusionImageLoader.Gray32ImagePlusLoader(), sliceValueMin, sliceValueMax );
+ final ArrayList< BasicViewSetup > setups = new ArrayList<>();
for ( int setupId = 0; setupId < channels.size(); ++setupId )
{
final String name = "fused c " + channels.get( setupId );
@@ -101,7 +100,7 @@ public class FusionResult
setups.add( setup );
}
desc = new SequenceDescriptionMinimal( timepoints, Entity.idMap( setups ), fusionLoader, null );
- final ArrayList< ViewRegistration > registrations = new ArrayList< ViewRegistration >();
+ final ArrayList< ViewRegistration > registrations = new ArrayList<>();
for ( final TimePoint timepoint : timepoints.getTimePointsOrdered() )
for ( final BasicViewSetup setup : setups )
registrations.add( new ViewRegistration( timepoint.getId(), setup.getId(), perTimePointFusionTransforms.get( timepoint.getId() ) ) );
diff --git a/src/main/java/bdv/ij/export/Scripting.java b/src/main/java/bdv/ij/export/Scripting.java
index 250149f1acbaacdb36a3cf1a3d05f699a1f6540b..e7f30ae7c10b33d04139e2f04fce84487b3211af 100644
--- a/src/main/java/bdv/ij/export/Scripting.java
+++ b/src/main/java/bdv/ij/export/Scripting.java
@@ -5,9 +5,6 @@ import java.util.ArrayList;
import java.util.List;
import java.util.Map;
-import mpicbg.spim.data.SpimDataException;
-import mpicbg.spim.io.ConfigurationParserException;
-import net.imglib2.realtransform.AffineTransform3D;
import bdv.export.ExportMipmapInfo;
import bdv.export.WriteSequenceToHdf5;
import bdv.ij.util.PluginHelper;
@@ -16,6 +13,9 @@ import bdv.img.hdf5.Partition;
import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal;
+import mpicbg.spim.data.SpimDataException;
+import mpicbg.spim.io.ConfigurationParserException;
+import net.imglib2.realtransform.AffineTransform3D;
public class Scripting
{
@@ -193,7 +193,7 @@ public class Scripting
spimData = aggregator.createSpimData( seqFile );
perSetupMipmapInfo = aggregator.getPerSetupMipmapInfo();
this.deflate = deflate;
- this.partitions = new ArrayList< Partition >( partitions );
+ this.partitions = new ArrayList<>( partitions );
}
public int numPartitions()
diff --git a/src/main/java/bdv/ij/export/SetupAggregator.java b/src/main/java/bdv/ij/export/SetupAggregator.java
index 6111c0dd3bd1cb75f9a4f41f294d0739294e94cf..b21d975da3db27e19f48c296a2657a215408b110 100644
--- a/src/main/java/bdv/ij/export/SetupAggregator.java
+++ b/src/main/java/bdv/ij/export/SetupAggregator.java
@@ -5,6 +5,11 @@ import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
+import bdv.export.ExportMipmapInfo;
+import bdv.export.WriteSequenceToHdf5;
+import bdv.ij.util.PluginHelper;
+import bdv.spimdata.SequenceDescriptionMinimal;
+import bdv.spimdata.SpimDataMinimal;
import mpicbg.spim.data.generic.XmlIoAbstractSpimData;
import mpicbg.spim.data.generic.base.Entity;
import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
@@ -19,11 +24,6 @@ import mpicbg.spim.data.sequence.TimePoint;
import mpicbg.spim.data.sequence.TimePoints;
import mpicbg.spim.data.sequence.ViewId;
import net.imglib2.img.cell.CellImg;
-import bdv.export.ExportMipmapInfo;
-import bdv.export.WriteSequenceToHdf5;
-import bdv.ij.util.PluginHelper;
-import bdv.spimdata.SequenceDescriptionMinimal;
-import bdv.spimdata.SpimDataMinimal;
/**
* Aggregate {@link BasicViewSetup setups}, i.e., SPIM source angles and fused
@@ -63,10 +63,10 @@ public class SetupAggregator
public SetupAggregator()
{
timepoints = null;
- registrations = new ArrayList< ViewRegistration >();
- setups = new ArrayList< ViewSetupWrapper >();
- setupImgLoaders = new ArrayList< BasicSetupImgLoader< ? > >();
- perSetupMipmapInfo = new HashMap< Integer, ExportMipmapInfo >();
+ registrations = new ArrayList<>();
+ setups = new ArrayList<>();
+ setupImgLoaders = new ArrayList<>();
+ perSetupMipmapInfo = new HashMap<>();
imgLoader = new BasicImgLoader()
{
@Override
diff --git a/src/main/java/bdv/ij/export/SpimRegistrationSequence.java b/src/main/java/bdv/ij/export/SpimRegistrationSequence.java
index 5a291b93bb315094bf317beee1a37665c6908208..55649650811640a44e3311fe8956a41c883bf5b4 100644
--- a/src/main/java/bdv/ij/export/SpimRegistrationSequence.java
+++ b/src/main/java/bdv/ij/export/SpimRegistrationSequence.java
@@ -7,6 +7,9 @@ import java.util.Map;
import org.scijava.vecmath.Point3f;
+import bdv.ij.export.imgloader.HuiskenImageLoader;
+import bdv.ij.export.imgloader.StackImageLoader;
+import bdv.spimdata.SequenceDescriptionMinimal;
import mpicbg.spim.data.generic.base.Entity;
import mpicbg.spim.data.generic.sequence.BasicImgLoader;
import mpicbg.spim.data.registration.ViewRegistration;
@@ -32,9 +35,6 @@ import net.imglib2.FinalRealInterval;
import net.imglib2.RealInterval;
import net.imglib2.realtransform.AffineTransform3D;
import spimopener.SPIMExperiment;
-import bdv.ij.export.imgloader.HuiskenImageLoader;
-import bdv.ij.export.imgloader.StackImageLoader;
-import bdv.spimdata.SequenceDescriptionMinimal;
public class SpimRegistrationSequence
{
@@ -81,7 +81,7 @@ public class SpimRegistrationSequence
protected static BasicImgLoader createImageLoader( final SPIMConfiguration conf, final ArrayList< ViewSetup > setups )
{
final int numTimepoints = conf.timepoints.length;
- final HashMap< ViewId, String > filenames = new HashMap< ViewId, String >();
+ final HashMap< ViewId, String > filenames = new HashMap<>();
for ( int timepoint = 0; timepoint < numTimepoints; ++timepoint )
{
final int timepointId = conf.timepoints[ timepoint ];
@@ -171,7 +171,7 @@ public class SpimRegistrationSequence
protected static ArrayList< ViewSetup > createViewSetups( final SPIMConfiguration conf )
{
- final ArrayList< ViewSetup > setups = new ArrayList< ViewSetup >();
+ final ArrayList< ViewSetup > setups = new ArrayList<>();
int setup_id = 0;
for ( int channelIndex = 0; channelIndex < conf.file[ 0 ].length; channelIndex++ )
for ( int angleIndex = 0; angleIndex < conf.file[ 0 ][ channelIndex ].length; angleIndex++ )
@@ -216,7 +216,7 @@ public class SpimRegistrationSequence
protected static TimePoints createTimePoints( final SPIMConfiguration conf )
{
- final ArrayList< TimePoint > timepoints = new ArrayList< TimePoint >();
+ final ArrayList< TimePoint > timepoints = new ArrayList<>();
for ( final int tp : conf.timepoints )
timepoints.add( new TimePoint( tp ) );
return new TimePoints( timepoints );
@@ -229,7 +229,7 @@ public class SpimRegistrationSequence
conf.cropOffsetZ = cropOffsetZ;
conf.scale = scale;
- final HashMap< Integer, AffineTransform3D > transforms = new HashMap< Integer, AffineTransform3D >();
+ final HashMap< Integer, AffineTransform3D > transforms = new HashMap<>();
if ( conf.timeLapseRegistration )
{
SPIMConfiguration refconf = conf;
@@ -334,7 +334,7 @@ public class SpimRegistrationSequence
protected static ViewRegistrations createViewRegistrations( final SPIMConfiguration conf, final ArrayList< ViewSetup > setups )
{
- final ArrayList< ViewRegistration > regs = new ArrayList< ViewRegistration >();
+ final ArrayList< ViewRegistration > regs = new ArrayList<>();
// for each time-point initialize the view structure, load&apply
// registrations, instantiate the View objects for Tracking
@@ -376,7 +376,7 @@ public class SpimRegistrationSequence
protected static ArrayList< Integer > makeList( final int[] ints )
{
- final ArrayList< Integer > list = new ArrayList< Integer >( ints.length );
+ final ArrayList< Integer > list = new ArrayList<>( ints.length );
for ( final int i : ints )
list.add( i );
return list;
diff --git a/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java b/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java
index de05de48fe97165473e02a19f341bca5c5c0fe93..5b01a1dd587d8e59d9b3f947577100656ed6144b 100644
--- a/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java
@@ -1,12 +1,11 @@
package bdv.ij.export.imgloader;
-import ij.ImagePlus;
-import io.scif.img.ImgIOException;
-import io.scif.img.ImgOpener;
-
import java.util.HashMap;
import java.util.Map.Entry;
+import ij.ImagePlus;
+import io.scif.img.ImgIOException;
+import io.scif.img.ImgOpener;
import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
import mpicbg.spim.data.generic.sequence.ImgLoaderHint;
import mpicbg.spim.data.sequence.FinalVoxelDimensions;
@@ -72,10 +71,10 @@ public class FusionImageLoader< T extends RealType< T > > implements ImgLoader
this.pattern = pattern;
this.numSlices = numSlices;
this.sliceLoader = sliceLoader;
- converter = new RealUnsignedShortConverter< T >( sliceValueMin, sliceValueMax );
+ converter = new RealUnsignedShortConverter<>( sliceValueMin, sliceValueMax );
this.factory = factory;
type = new UnsignedShortType();
- setupIdToSetupImgLoader = new HashMap< Integer, SetupLoader >();
+ setupIdToSetupImgLoader = new HashMap<>();
for ( final Entry< Integer, Integer > entry : setupIdToChannelId.entrySet() )
setupIdToSetupImgLoader.put( entry.getKey(), new SetupLoader( entry.getValue() ) );
}
@@ -96,7 +95,7 @@ public class FusionImageLoader< T extends RealType< T > > implements ImgLoader
public ArrayImgLoader( final T type )
{
opener = new ImgOpener();
- factory = new ArrayImgFactory< T >();
+ factory = new ArrayImgFactory<>();
this.type = type;
}
diff --git a/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java b/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java
index 2cbc55dc430cb439f34111b3fafa94a3ff43d916..8dc85ba386139df45dd5af513d4bde0a2cdaafc0 100644
--- a/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java
@@ -1,11 +1,10 @@
package bdv.ij.export.imgloader;
-import ij.ImagePlus;
-
import java.io.File;
import java.util.HashMap;
import java.util.Map.Entry;
+import ij.ImagePlus;
import mpicbg.spim.data.generic.sequence.BasicImgLoader;
import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
import mpicbg.spim.data.generic.sequence.ImgLoaderHint;
@@ -40,7 +39,7 @@ public class HuiskenImageLoader implements BasicImgLoader
{
expFile = file;
exp = null;
- setupIdToSetupImgLoader = new HashMap< Integer, SetupLoader >();
+ setupIdToSetupImgLoader = new HashMap<>();
for ( final Entry< Integer, ViewSetup > entry : setups.entrySet() )
setupIdToSetupImgLoader.put( entry.getKey(), new SetupLoader( entry.getValue() ) );
}
@@ -98,7 +97,7 @@ public class HuiskenImageLoader implements BasicImgLoader
final float zStretching = ( float ) ( exp.pd / exp.pw );
final double[] calibration = new double[] { 1, 1, zStretching };
- return new ImgPlus< UnsignedShortType >( img, name, axes, calibration );
+ return new ImgPlus<>( img, name, axes, calibration );
}
@Override
diff --git a/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java b/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java
index 01f80652ca3d80aee18d609ad2bf6e7ed4c058d8..8d5192cc7549ac8df5a2b439c7a6b4fa0c1f1ce7 100644
--- a/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java
@@ -1,9 +1,11 @@
package bdv.ij.export.imgloader;
-import ij.ImagePlus;
-
import java.util.ArrayList;
+import bdv.img.cache.VolatileGlobalCellCache;
+import bdv.img.imagestack.ImageStackImageLoader;
+import bdv.img.virtualstack.VirtualStackImageLoader;
+import ij.ImagePlus;
import mpicbg.spim.data.generic.sequence.BasicImgLoader;
import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
import mpicbg.spim.data.generic.sequence.ImgLoaderHint;
@@ -19,9 +21,6 @@ import net.imglib2.type.Type;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.UnsignedShortType;
import net.imglib2.type.numeric.real.FloatType;
-import bdv.img.cache.VolatileGlobalCellCache;
-import bdv.img.imagestack.ImageStackImageLoader;
-import bdv.img.virtualstack.VirtualStackImageLoader;
/**
* This {@link BasicImgLoader} implementation returns a wrapped, converted
@@ -51,9 +50,9 @@ public class ImagePlusImgLoader< T extends Type< T > > implements TypedBasicImgL
if( imp.getType() != ImagePlus.GRAY8 )
throw new RuntimeException( "expected ImagePlus type GRAY8" );
if ( imp.getStack() != null && imp.getStack().isVirtual() )
- return new ImagePlusImgLoader< UnsignedShortType >( imp, VirtualStackImageLoader.createUnsignedByteInstance( imp ), minMaxOption, min, max, new UnsignedShortType(), new RealUnsignedShortConverterFactory() );
+ return new ImagePlusImgLoader<>( imp, VirtualStackImageLoader.createUnsignedByteInstance( imp ), minMaxOption, min, max, new UnsignedShortType(), new RealUnsignedShortConverterFactory() );
else
- return new ImagePlusImgLoader< UnsignedShortType >( imp, ImageStackImageLoader.createUnsignedByteInstance( imp ), minMaxOption, min, max, new UnsignedShortType(), new RealUnsignedShortConverterFactory() );
+ return new ImagePlusImgLoader<>( imp, ImageStackImageLoader.createUnsignedByteInstance( imp ), minMaxOption, min, max, new UnsignedShortType(), new RealUnsignedShortConverterFactory() );
}
public static ImagePlusImgLoader< FloatType > createFloatFromGray8( final ImagePlus imp, final MinMaxOption minMaxOption, final double min, final double max )
@@ -61,9 +60,9 @@ public class ImagePlusImgLoader< T extends Type< T > > implements TypedBasicImgL
if( imp.getType() != ImagePlus.GRAY8 )
throw new RuntimeException( "expected ImagePlus type GRAY8" );
if ( imp.getStack() != null && imp.getStack().isVirtual() )
- return new ImagePlusImgLoader< FloatType >( imp, VirtualStackImageLoader.createUnsignedByteInstance( imp ), minMaxOption, min, max, new FloatType(), new RealFloatConverterFactory() );
+ return new ImagePlusImgLoader<>( imp, VirtualStackImageLoader.createUnsignedByteInstance( imp ), minMaxOption, min, max, new FloatType(), new RealFloatConverterFactory() );
else
- return new ImagePlusImgLoader< FloatType >( imp, ImageStackImageLoader.createUnsignedByteInstance( imp ), minMaxOption, min, max, new FloatType(), new RealFloatConverterFactory() );
+ return new ImagePlusImgLoader<>( imp, ImageStackImageLoader.createUnsignedByteInstance( imp ), minMaxOption, min, max, new FloatType(), new RealFloatConverterFactory() );
}
public static ImagePlusImgLoader< UnsignedShortType > createGray16( final ImagePlus imp, final MinMaxOption minMaxOption, final double min, final double max )
@@ -71,9 +70,9 @@ public class ImagePlusImgLoader< T extends Type< T > > implements TypedBasicImgL
if( imp.getType() != ImagePlus.GRAY16 )
throw new RuntimeException( "expected ImagePlus type GRAY16" );
if ( imp.getStack() != null && imp.getStack().isVirtual() )
- return new ImagePlusImgLoader< UnsignedShortType >( imp, VirtualStackImageLoader.createUnsignedShortInstance( imp ), minMaxOption, min, max, new UnsignedShortType(), new RealUnsignedShortConverterFactory() );
+ return new ImagePlusImgLoader<>( imp, VirtualStackImageLoader.createUnsignedShortInstance( imp ), minMaxOption, min, max, new UnsignedShortType(), new RealUnsignedShortConverterFactory() );
else
- return new ImagePlusImgLoader< UnsignedShortType >( imp, ImageStackImageLoader.createUnsignedShortInstance( imp ), minMaxOption, min, max, new UnsignedShortType(), new RealUnsignedShortConverterFactory() );
+ return new ImagePlusImgLoader<>( imp, ImageStackImageLoader.createUnsignedShortInstance( imp ), minMaxOption, min, max, new UnsignedShortType(), new RealUnsignedShortConverterFactory() );
}
public static ImagePlusImgLoader< UnsignedShortType > createGray32( final ImagePlus imp, final MinMaxOption minMaxOption, final double min, final double max )
@@ -81,9 +80,9 @@ public class ImagePlusImgLoader< T extends Type< T > > implements TypedBasicImgL
if( imp.getType() != ImagePlus.GRAY32 )
throw new RuntimeException( "expected ImagePlus type GRAY32" );
if ( imp.getStack() != null && imp.getStack().isVirtual() )
- return new ImagePlusImgLoader< UnsignedShortType >( imp, VirtualStackImageLoader.createFloatInstance( imp ), minMaxOption, min, max, new UnsignedShortType(), new RealUnsignedShortConverterFactory() );
+ return new ImagePlusImgLoader<>( imp, VirtualStackImageLoader.createFloatInstance( imp ), minMaxOption, min, max, new UnsignedShortType(), new RealUnsignedShortConverterFactory() );
else
- return new ImagePlusImgLoader< UnsignedShortType >( imp, ImageStackImageLoader.createFloatInstance( imp ), minMaxOption, min, max, new UnsignedShortType(), new RealUnsignedShortConverterFactory() );
+ return new ImagePlusImgLoader<>( imp, ImageStackImageLoader.createFloatInstance( imp ), minMaxOption, min, max, new UnsignedShortType(), new RealUnsignedShortConverterFactory() );
}
protected final ImagePlus imp;
@@ -112,7 +111,7 @@ public class ImagePlusImgLoader< T extends Type< T > > implements TypedBasicImgL
@Override
public < S extends RealType< S > & NativeType< S > > Converter< S, UnsignedShortType > create( final double min, final double max )
{
- return new RealUnsignedShortConverter< S >( min, max );
+ return new RealUnsignedShortConverter<>( min, max );
}
}
@@ -121,7 +120,7 @@ public class ImagePlusImgLoader< T extends Type< T > > implements TypedBasicImgL
@Override
public < S extends RealType< S > & NativeType< S > > Converter< S, FloatType > create( final double min, final double max )
{
- return new RealFloatConverter< S >();
+ return new RealFloatConverter<>();
}
}
@@ -139,9 +138,9 @@ public class ImagePlusImgLoader< T extends Type< T > > implements TypedBasicImgL
this.converterFactory = converterFactory;
final int numSetups = imp.getNChannels();
- setupImgLoaders = new ArrayList< SetupImgLoader< ? > >();
+ setupImgLoaders = new ArrayList<>();
for ( int setupId = 0; setupId < numSetups; ++setupId )
- setupImgLoaders.add( new SetupImgLoader< S >( loader.getSetupImgLoader( setupId ) ) );
+ setupImgLoaders.add( new SetupImgLoader<>( loader.getSetupImgLoader( setupId ) ) );
if ( loader instanceof VirtualStackImageLoader )
this.loadercache = ( ( VirtualStackImageLoader< ?, ?, ? > ) loader ).getCache();
diff --git a/src/main/java/bdv/ij/export/imgloader/LegacyStackImageLoader.java b/src/main/java/bdv/ij/export/imgloader/LegacyStackImageLoader.java
index 954547fccac16c0e60e81ceef0f997c6d669017d..c832d531e349749484db9e5c0fc4fa7de2cc35dc 100644
--- a/src/main/java/bdv/ij/export/imgloader/LegacyStackImageLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/LegacyStackImageLoader.java
@@ -1,12 +1,15 @@
package bdv.ij.export.imgloader;
+import java.util.HashMap;
+
+import org.scijava.Context;
+import org.scijava.app.AppService;
+import org.scijava.app.StatusService;
+
import ij.ImagePlus;
import io.scif.SCIFIOService;
import io.scif.img.ImgIOException;
import io.scif.img.ImgOpener;
-
-import java.util.HashMap;
-
import mpicbg.spim.data.legacy.LegacyBasicImgLoader;
import mpicbg.spim.data.sequence.ImgLoader;
import mpicbg.spim.data.sequence.ViewDescription;
@@ -21,10 +24,6 @@ import net.imglib2.meta.ImgPlus;
import net.imglib2.type.numeric.integer.UnsignedByteType;
import net.imglib2.type.numeric.integer.UnsignedShortType;
-import org.scijava.Context;
-import org.scijava.app.AppService;
-import org.scijava.app.StatusService;
-
/**
* This {@link ImgLoader} loads images that represent a 3D stack in a single
@@ -52,7 +51,7 @@ public class LegacyStackImageLoader implements LegacyBasicImgLoader< UnsignedSho
this.filenames = filenames;
this.useImageJOpener = useImageJOpener;
opener = useImageJOpener ? null : new ImgOpener( new Context( SCIFIOService.class, AppService.class, StatusService.class ) );
- factory = new ArrayImgFactory< UnsignedShortType >();
+ factory = new ArrayImgFactory<>();
type = new UnsignedShortType();
}
@@ -64,12 +63,12 @@ public class LegacyStackImageLoader implements LegacyBasicImgLoader< UnsignedSho
{
final ImagePlus imp = new ImagePlus( fn );
if ( imp.getType() == ImagePlus.GRAY16 )
- return new ImgPlus< UnsignedShortType >( ImageJFunctions.wrapShort( imp ) );
+ return new ImgPlus<>( ImageJFunctions.wrapShort( imp ) );
else if ( imp.getType() == ImagePlus.GRAY8 )
{
System.out.println( "wrapping" );
- return new ImgPlus< UnsignedShortType >(
- new ImgView< UnsignedShortType >(
+ return new ImgPlus<>(
+ new ImgView<>(
Converters.convert(
( RandomAccessibleInterval<UnsignedByteType> ) ImageJFunctions.wrapByte( imp ),
new Converter< UnsignedByteType, UnsignedShortType >() {
diff --git a/src/main/java/bdv/ij/export/tiles/CellVoyagerDataExporter.java b/src/main/java/bdv/ij/export/tiles/CellVoyagerDataExporter.java
index 29ce30f18c4673fd4876d2fb112a869d7ed36aa6..b4a8c636cddd3ec2f1a61e03d4465a34e0f9da00 100644
--- a/src/main/java/bdv/ij/export/tiles/CellVoyagerDataExporter.java
+++ b/src/main/java/bdv/ij/export/tiles/CellVoyagerDataExporter.java
@@ -1,26 +1,11 @@
package bdv.ij.export.tiles;
-import ij.IJ;
-
import java.awt.Color;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
-import mpicbg.spim.data.generic.base.Entity;
-import mpicbg.spim.data.generic.sequence.BasicViewSetup;
-import mpicbg.spim.data.registration.ViewRegistration;
-import mpicbg.spim.data.registration.ViewRegistrations;
-import mpicbg.spim.data.sequence.Channel;
-import mpicbg.spim.data.sequence.FinalVoxelDimensions;
-import mpicbg.spim.data.sequence.TimePoint;
-import mpicbg.spim.data.sequence.TimePoints;
-import mpicbg.spim.data.sequence.VoxelDimensions;
-import net.imglib2.Dimensions;
-import net.imglib2.FinalDimensions;
-import net.imglib2.realtransform.AffineTransform3D;
-
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
@@ -33,6 +18,19 @@ import bdv.img.hdf5.Hdf5ImageLoader;
import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal;
import bdv.spimdata.XmlIoSpimDataMinimal;
+import ij.IJ;
+import mpicbg.spim.data.generic.base.Entity;
+import mpicbg.spim.data.generic.sequence.BasicViewSetup;
+import mpicbg.spim.data.registration.ViewRegistration;
+import mpicbg.spim.data.registration.ViewRegistrations;
+import mpicbg.spim.data.sequence.Channel;
+import mpicbg.spim.data.sequence.FinalVoxelDimensions;
+import mpicbg.spim.data.sequence.TimePoint;
+import mpicbg.spim.data.sequence.TimePoints;
+import mpicbg.spim.data.sequence.VoxelDimensions;
+import net.imglib2.Dimensions;
+import net.imglib2.FinalDimensions;
+import net.imglib2.realtransform.AffineTransform3D;
public class CellVoyagerDataExporter
{
@@ -91,7 +89,7 @@ public class CellVoyagerDataExporter
public List< ChannelInfo > readInfo()
{
- final List< ChannelInfo > channels = new ArrayList< ChannelInfo >();
+ final List< ChannelInfo > channels = new ArrayList<>();
final Element root = document.getRootElement();
@@ -161,7 +159,7 @@ public class CellVoyagerDataExporter
double ymin = Double.POSITIVE_INFINITY;
double xmax = Double.NEGATIVE_INFINITY;
double ymax = Double.NEGATIVE_INFINITY;
- final ArrayList< double[] > offsetsUm = new ArrayList< double[] >();
+ final ArrayList< double[] > offsetsUm = new ArrayList<>();
for ( final Element fieldElement : fieldElements )
{
@@ -194,7 +192,7 @@ public class CellVoyagerDataExporter
}
// Convert in pixel position
- final List< long[] > offsets = new ArrayList< long[] >();
+ final List< long[] > offsets = new ArrayList<>();
for ( final double[] offsetUm : offsetsUm )
{
final long x = ( long ) ( ( offsetUm[ 0 ] - xmin ) / ( channelInfo.unmagnifiedPixelWidth / magnification ) );
@@ -235,7 +233,7 @@ public class CellVoyagerDataExporter
final Element root = document.getRootElement();
final int nTimePoints = Integer.parseInt( root.getChild( "TimelapsCondition" ).getChildText( "Iteration" ) );
- final List< TimePoint > timepoints = new ArrayList< TimePoint >( nTimePoints );
+ final List< TimePoint > timepoints = new ArrayList<>( nTimePoints );
for ( int i = 0; i < nTimePoints; i++ )
{
timepoints.add( new TimePoint( Integer.valueOf( i ) ) );
@@ -275,7 +273,7 @@ public class CellVoyagerDataExporter
* Create view setups
*/
- final List< BasicViewSetup > setups = new ArrayList< BasicViewSetup >( channelInfos.size() );
+ final List< BasicViewSetup > setups = new ArrayList<>( channelInfos.size() );
int viewSetupIndex = 0;
for ( final ChannelInfo channelInfo : channelInfos )
{
@@ -330,7 +328,7 @@ public class CellVoyagerDataExporter
* Build views
*/
- final ArrayList< ViewRegistration > registrations = new ArrayList< ViewRegistration >();
+ final ArrayList< ViewRegistration > registrations = new ArrayList<>();
for ( int setupIndex = 0; setupIndex < setups.size(); setupIndex++ )
{
diff --git a/src/main/java/bdv/ij/export/tiles/LegacyTileImgLoader.java b/src/main/java/bdv/ij/export/tiles/LegacyTileImgLoader.java
index cf56ec75b622c2d6612781abe6b1520bcd23d796..fdde49d7738d1542fcc5b30fe930ff2663ebd397 100644
--- a/src/main/java/bdv/ij/export/tiles/LegacyTileImgLoader.java
+++ b/src/main/java/bdv/ij/export/tiles/LegacyTileImgLoader.java
@@ -1,7 +1,5 @@
package bdv.ij.export.tiles;
-import ij.ImagePlus;
-
import java.io.File;
import java.io.IOException;
import java.util.HashMap;
@@ -10,6 +8,15 @@ import java.util.List;
import java.util.Map;
import java.util.TreeMap;
+import org.jdom2.DataConversionException;
+import org.jdom2.Document;
+import org.jdom2.Element;
+import org.jdom2.JDOMException;
+import org.jdom2.Namespace;
+import org.jdom2.input.SAXBuilder;
+
+import bdv.ij.export.tiles.CellVoyagerDataExporter.ChannelInfo;
+import ij.ImagePlus;
import mpicbg.spim.data.legacy.LegacyBasicImgLoader;
import mpicbg.spim.data.sequence.ViewId;
import net.imglib2.Cursor;
@@ -22,15 +29,6 @@ import net.imglib2.img.basictypeaccess.array.ShortArray;
import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.type.numeric.integer.UnsignedShortType;
-import org.jdom2.DataConversionException;
-import org.jdom2.Document;
-import org.jdom2.Element;
-import org.jdom2.JDOMException;
-import org.jdom2.Namespace;
-import org.jdom2.input.SAXBuilder;
-
-import bdv.ij.export.tiles.CellVoyagerDataExporter.ChannelInfo;
-
public class LegacyTileImgLoader implements LegacyBasicImgLoader< UnsignedShortType >
{
@@ -84,7 +82,7 @@ public class LegacyTileImgLoader implements LegacyBasicImgLoader< UnsignedShortT
// Map of z -> all the tiles. The tiles are a map of field index ->
// filename
- final TreeMap< Double, Map< Integer, String > > filenames = new TreeMap< Double, Map< Integer, String > >();
+ final TreeMap< Double, Map< Integer, String > > filenames = new TreeMap<>();
final Element root = document.getRootElement();
for ( final Element element : root.getChildren( "MeasurementRecord", NAMESPACE ) )
@@ -118,7 +116,7 @@ public class LegacyTileImgLoader implements LegacyBasicImgLoader< UnsignedShortT
Map< Integer, String > tilesAtZ = filenames.get( dz );
if ( null == tilesAtZ )
{
- tilesAtZ = new HashMap< Integer, String >();
+ tilesAtZ = new HashMap<>();
filenames.put( dz, tilesAtZ );
}
tilesAtZ.put( field, filename );
diff --git a/src/main/java/bdv/ij/util/PluginHelper.java b/src/main/java/bdv/ij/util/PluginHelper.java
index 9cd78813502179f93c808d28417f0d597c0e946c..a70660bdd7bb8657fd7e65a10727dc0a875a499b 100644
--- a/src/main/java/bdv/ij/util/PluginHelper.java
+++ b/src/main/java/bdv/ij/util/PluginHelper.java
@@ -1,7 +1,5 @@
package bdv.ij.util;
-import ij.Prefs;
-
import java.awt.Button;
import java.awt.FileDialog;
import java.awt.FlowLayout;
@@ -23,6 +21,7 @@ import javax.swing.JFileChooser;
import javax.swing.filechooser.FileFilter;
import fiji.util.gui.GenericDialogPlus;
+import ij.Prefs;
public class PluginHelper
{
@@ -146,7 +145,7 @@ public class PluginHelper
final Pattern pattern = Pattern.compile( regex );
final Matcher matcher = pattern.matcher( s );
- final ArrayList< int[] > tmp = new ArrayList< int[] >();
+ final ArrayList< int[] > tmp = new ArrayList<>();
while ( matcher.find() )
{
final int[] resolution = new int[] { Integer.parseInt( matcher.group( 1 ) ), Integer.parseInt( matcher.group( 2 ) ), Integer.parseInt( matcher.group( 3 ) ) };
diff --git a/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java b/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java
index 9edcce0d48479748a876274a520ae38529d4e8b0..43affc871fe4d5f5ccc9f5a8e1b521d32dad44e4 100644
--- a/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java
+++ b/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java
@@ -1,9 +1,8 @@
package bdv.img.imagestack;
-import ij.ImagePlus;
-
import java.util.ArrayList;
+import ij.ImagePlus;
import mpicbg.spim.data.generic.sequence.BasicImgLoader;
import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
import mpicbg.spim.data.generic.sequence.ImgLoaderHint;
@@ -110,7 +109,7 @@ public abstract class ImageStackImageLoader< T extends NumericType< T > & Native
this.imp = imp;
this.dim = new long[] { imp.getWidth(), imp.getHeight(), imp.getNSlices() };
final int numSetups = imp.getNChannels();
- setupImgLoaders = new ArrayList< SetupImgLoader >();
+ setupImgLoaders = new ArrayList<>();
for ( int setupId = 0; setupId < numSetups; ++setupId )
setupImgLoaders.add( new SetupImgLoader( setupId ) );
}
diff --git a/src/main/java/bdv/img/virtualstack/VirtualStackImageLoader.java b/src/main/java/bdv/img/virtualstack/VirtualStackImageLoader.java
index c103ff3c232b064ca551cff444b410dd0f282c71..93618ec5adee8f15b2856777b344a177eaacda3f 100644
--- a/src/main/java/bdv/img/virtualstack/VirtualStackImageLoader.java
+++ b/src/main/java/bdv/img/virtualstack/VirtualStackImageLoader.java
@@ -1,9 +1,17 @@
package bdv.img.virtualstack;
-import ij.ImagePlus;
-
import java.util.ArrayList;
+import bdv.AbstractViewerSetupImgLoader;
+import bdv.ViewerImgLoader;
+import bdv.img.cache.CacheArrayLoader;
+import bdv.img.cache.CacheHints;
+import bdv.img.cache.CachedCellImg;
+import bdv.img.cache.LoadingStrategy;
+import bdv.img.cache.VolatileGlobalCellCache;
+import bdv.img.cache.VolatileImgCells;
+import bdv.img.cache.VolatileImgCells.CellCache;
+import ij.ImagePlus;
import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
import mpicbg.spim.data.generic.sequence.ImgLoaderHint;
import mpicbg.spim.data.generic.sequence.TypedBasicImgLoader;
@@ -27,15 +35,6 @@ import net.imglib2.type.volatiles.VolatileFloatType;
import net.imglib2.type.volatiles.VolatileUnsignedByteType;
import net.imglib2.type.volatiles.VolatileUnsignedShortType;
import net.imglib2.util.Fraction;
-import bdv.AbstractViewerSetupImgLoader;
-import bdv.ViewerImgLoader;
-import bdv.img.cache.CacheArrayLoader;
-import bdv.img.cache.CacheHints;
-import bdv.img.cache.CachedCellImg;
-import bdv.img.cache.LoadingStrategy;
-import bdv.img.cache.VolatileGlobalCellCache;
-import bdv.img.cache.VolatileImgCells;
-import bdv.img.cache.VolatileImgCells.CellCache;
/**
* ImageLoader backed by a ImagePlus. The ImagePlus may be virtual and in
@@ -162,7 +161,7 @@ public abstract class VirtualStackImageLoader< T extends NativeType< T >, V exte
final int numTimepoints = imp.getNFrames();
final int numSetups = imp.getNChannels();
cache = new VolatileGlobalCellCache( numTimepoints, numSetups, 1, 1 );
- setupImgLoaders = new ArrayList< SetupImgLoader >();
+ setupImgLoaders = new ArrayList<>();
for ( int setupId = 0; setupId < numSetups; ++setupId )
setupImgLoaders.add( new SetupImgLoader( setupId, type, volatileType ) );
}
@@ -221,9 +220,9 @@ public abstract class VirtualStackImageLoader< T extends NativeType< T >, V exte
{
final int priority = 0;
final CacheHints cacheHints = new CacheHints( loadingStrategy, priority, false );
- final CellCache< A > c = cache.new VolatileCellCache< A >( view.getTimePointId(), view.getViewSetupId(), level, cacheHints, loader );
- final VolatileImgCells< A > cells = new VolatileImgCells< A >( c, new Fraction(), dimensions, cellDimensions );
- final CachedCellImg< T, A > img = new CachedCellImg< T, A >( cells );
+ final CellCache< A > c = cache.new VolatileCellCache<>( view.getTimePointId(), view.getViewSetupId(), level, cacheHints, loader );
+ final VolatileImgCells< A > cells = new VolatileImgCells<>( c, new Fraction(), dimensions, cellDimensions );
+ final CachedCellImg< T, A > img = new CachedCellImg<>( cells );
return img;
}