diff --git a/src/main/java/bdv/ij/BigDataBrowserPlugIn.java b/src/main/java/bdv/ij/BigDataBrowserPlugIn.java
index 96e072ab78d851f9d11ff672a2a8ab4e8746197c..c1102e55177aac812801e8bd35084ae9ca26be3d 100644
--- a/src/main/java/bdv/ij/BigDataBrowserPlugIn.java
+++ b/src/main/java/bdv/ij/BigDataBrowserPlugIn.java
@@ -37,7 +37,7 @@ import bdv.ij.util.ProgressWriterIJ;
import com.google.gson.stream.JsonReader;
/**
- * @author HongKee Moon <moon@mpi-cbg.de>
+ * @author HongKee Moon <moon@mpi-cbg.de>
*/
public class BigDataBrowserPlugIn implements PlugIn
{
diff --git a/src/main/java/bdv/ij/ExportImagePlusPlugIn.java b/src/main/java/bdv/ij/ExportImagePlusPlugIn.java
index 3413f8be778b6d4e59880f7b799fc2933624e56e..5300891c06769dc56c8165294ccd985113091050 100644
--- a/src/main/java/bdv/ij/ExportImagePlusPlugIn.java
+++ b/src/main/java/bdv/ij/ExportImagePlusPlugIn.java
@@ -49,7 +49,7 @@ import bdv.spimdata.XmlIoSpimDataMinimal;
/**
* ImageJ plugin to export the current image to xml/hdf5.
*
- * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
public class ExportImagePlusPlugIn implements PlugIn
{
diff --git a/src/main/java/bdv/ij/ImportPlugIn.java b/src/main/java/bdv/ij/ImportPlugIn.java
index 34b7a3a56520554a71ff174e220f55f191b9c97d..013273945a3a1fdec09ad177f143ba22157dacb0 100644
--- a/src/main/java/bdv/ij/ImportPlugIn.java
+++ b/src/main/java/bdv/ij/ImportPlugIn.java
@@ -35,7 +35,7 @@ import bdv.spimdata.XmlIoSpimDataMinimal;
/**
* ImageJ plugin to import a raw image from xml/hdf5.
*
- * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
public class ImportPlugIn implements PlugIn
{
diff --git a/src/main/java/bdv/ij/OpenImagePlusPlugIn.java b/src/main/java/bdv/ij/OpenImagePlusPlugIn.java
index ba91223d7ef033b9dc21b84a83969344c849684f..f26f431a852b434450740c18dc5c0e2c6bd30b8b 100644
--- a/src/main/java/bdv/ij/OpenImagePlusPlugIn.java
+++ b/src/main/java/bdv/ij/OpenImagePlusPlugIn.java
@@ -38,7 +38,7 @@ import bdv.viewer.VisibilityAndGrouping;
/**
* ImageJ plugin to show the current image in BigDataViewer.
*
- * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
public class OpenImagePlusPlugIn implements PlugIn
{
diff --git a/src/main/java/bdv/ij/export/FixAbsolutePathsInHdf5Partitions.java b/src/main/java/bdv/ij/export/FixAbsolutePathsInHdf5Partitions.java
index 60c3dc9956bacad1fa4475f95d65f03b37b23079..a671318f17d1c670eaabcb432f544368d3b12f78 100644
--- a/src/main/java/bdv/ij/export/FixAbsolutePathsInHdf5Partitions.java
+++ b/src/main/java/bdv/ij/export/FixAbsolutePathsInHdf5Partitions.java
@@ -27,7 +27,7 @@ import bdv.spimdata.XmlIoSpimDataMinimal;
* be written (the original master hdf5 will not be overwritten). To actually
* use the fixed version rename it (remove the "FIXED" postfix).
*
- * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
public class FixAbsolutePathsInHdf5Partitions
{
diff --git a/src/main/java/bdv/ij/export/FusionResult.java b/src/main/java/bdv/ij/export/FusionResult.java
index 890009c13be3c7cedbe8060b00b5104c4f39cf5d..5475db5bef1ee388b4a3f91b6bd714f1aa207ae1 100644
--- a/src/main/java/bdv/ij/export/FusionResult.java
+++ b/src/main/java/bdv/ij/export/FusionResult.java
@@ -117,4 +117,4 @@ public class FusionResult
{
return regs;
}
-}
\ No newline at end of file
+}
diff --git a/src/main/java/bdv/ij/export/Scripting.java b/src/main/java/bdv/ij/export/Scripting.java
index 41bfde323326533d79f366b42d2a5660ab1deb08..250149f1acbaacdb36a3cf1a3d05f699a1f6540b 100644
--- a/src/main/java/bdv/ij/export/Scripting.java
+++ b/src/main/java/bdv/ij/export/Scripting.java
@@ -127,7 +127,7 @@ public class Scripting
* @param numSlices
* @param sliceValueMin
* @param sliceValueMax
- * @param fusionTransform
+ * @param fusionTransforms
* @return
*/
public static FusionResult createFusionResult(
@@ -150,10 +150,10 @@ public class Scripting
* represents the full dataset.
* @param timepointsPerPartition
* how many timepoints should each partition contain (if this is
- * ≤0, put do not split timepoints across partitions).
+ * ≤0, put do not split timepoints across partitions).
* @param setupsPerPartition
* how many setups should each partition contain (if this is
- * ≤0, put do not split setups across partitions).
+ * ≤0, put do not split setups across partitions).
* @param xmlFilename
* path to the xml file to which the sequence will be saved. This
* is used to generate paths for the partitions.
diff --git a/src/main/java/bdv/ij/export/SetupAggregator.java b/src/main/java/bdv/ij/export/SetupAggregator.java
index a5da226734ed5ddfa179924db52d04ded13ff9a0..6111c0dd3bd1cb75f9a4f41f294d0739294e94cf 100644
--- a/src/main/java/bdv/ij/export/SetupAggregator.java
+++ b/src/main/java/bdv/ij/export/SetupAggregator.java
@@ -5,6 +5,7 @@ import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
+import mpicbg.spim.data.generic.XmlIoAbstractSpimData;
import mpicbg.spim.data.generic.base.Entity;
import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
import mpicbg.spim.data.generic.sequence.BasicImgLoader;
@@ -18,13 +19,11 @@ 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 net.imglib2.realtransform.AffineTransform3D;
import bdv.export.ExportMipmapInfo;
import bdv.export.WriteSequenceToHdf5;
import bdv.ij.util.PluginHelper;
import bdv.spimdata.SequenceDescriptionMinimal;
import bdv.spimdata.SpimDataMinimal;
-import bdv.spimdata.XmlIoSpimDataMinimal;
/**
* Aggregate {@link BasicViewSetup setups}, i.e., SPIM source angles and fused
@@ -33,7 +32,7 @@ import bdv.spimdata.XmlIoSpimDataMinimal;
*
* Note, that added setups are assigned new, consecutive ids starting from 0.
*
- * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
public class SetupAggregator
{
@@ -136,7 +135,7 @@ public class SetupAggregator
* Create a {@link SpimDataMinimal} for the setups currently aggregated.
* This can be used to write the sequence (see {@link WriteSequenceToHdf5}
* and
- * {@link XmlIoSpimDataMinimal#toXml(bdv.spimdata.SpimDataMinimal, File)}.
+ * {@link XmlIoAbstractSpimData#toXml(mpicbg.spim.data.generic.AbstractSpimData, File)}
*
* @param basePath
* @return a {@link SpimDataMinimal} with the currently aggregated setups.
@@ -170,7 +169,7 @@ public class SetupAggregator
*
* @param sequence
* a registered spim sequence. see
- * {@link Scripting#createSpimRegistrationSequence(String, String, String, String, int, boolean, double)}
+ * {@link Scripting#createSpimRegistrationSequence(String, String, String, String, String, int, boolean, double)}
* @param setupIndex
* which of the setups of the spim sequence to add.
* @param resolutionsString
@@ -213,7 +212,7 @@ public class SetupAggregator
*
* @param sequence
* a registered spim sequence. see
- * {@link Scripting#createSpimRegistrationSequence(String, String, String, String, int, boolean, double)}
+ * {@link Scripting#createSpimRegistrationSequence(String, String, String, String, String, int, boolean, double)}
* @param setupIndex
* which of the setups of the spim sequence to add.
* @param resolutions
@@ -248,7 +247,7 @@ public class SetupAggregator
*
* @param sequence
* a registered spim sequence. see
- * {@link Scripting#createSpimRegistrationSequence(String, String, String, String, int, boolean, double)}
+ * {@link Scripting#createSpimRegistrationSequence(String, String, String, String, String, int, boolean, double)}
* @param resolutionsString
* the set of resolutions to store, formatted like
* "{1,1,1}, {2,2,1}, {4,4,4}" where each "{...}" defines one
@@ -279,7 +278,7 @@ public class SetupAggregator
*
* @param sequence
* a registered spim sequence. see
- * {@link Scripting#createSpimRegistrationSequence(String, String, String, String, int, boolean, double)}
+ * {@link Scripting#createSpimRegistrationSequence(String, String, String, String, String, int, boolean, double)}
* @param resolutions
* the set of resolutions to store. each nested int[] array
* defines one resolution.
@@ -308,7 +307,7 @@ public class SetupAggregator
*
* @param fusionResult
* a fused spim sequence.
- * {@link Scripting#createFusionResult(SpimRegistrationSequence, String, String, int, double, double, AffineTransform3D)}
+ * {@link Scripting#createFusionResult(SpimRegistrationSequence, String, String, int, double, double, Map)}
* @param resolutionsString
* the set of resolutions to store, formatted like
* "{1,1,1}, {2,2,1}, {4,4,4}" where each "{...}" defines one
@@ -347,7 +346,7 @@ public class SetupAggregator
*
* @param fusionResult
* a fused spim sequence.
- * {@link Scripting#createFusionResult(SpimRegistrationSequence, String, String, int, double, double, AffineTransform3D)}
+ * {@link Scripting#createSpimRegistrationSequence(String, String, String, String, String, int, boolean, double)}
* @param resolutions
* the set of resolutions to store. each nested int[] array
* defines one resolution.
@@ -362,4 +361,4 @@ public class SetupAggregator
for( final BasicViewSetup setup : fusionResult.getSequenceDescription().getViewSetupsOrdered() )
add( setup, fusionResult.getSequenceDescription(), fusionResult.getViewRegistrations(), resolutions, subdivisions );
}
-}
\ No newline at end of file
+}
diff --git a/src/main/java/bdv/ij/export/ViewSetupWrapper.java b/src/main/java/bdv/ij/export/ViewSetupWrapper.java
index 87772ef78f6505bd00df42fe7b77a8059f6d3617..ebbb167838e33d821266fcb7b13d0a25295e8f2d 100644
--- a/src/main/java/bdv/ij/export/ViewSetupWrapper.java
+++ b/src/main/java/bdv/ij/export/ViewSetupWrapper.java
@@ -11,7 +11,7 @@ import mpicbg.spim.data.sequence.ViewSetup;
* Stores the {@link ViewSetup setup}'s original id and {@link SequenceDescription}.
* For example, this can be used to access the original {@link ImgLoader}.
*
- * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
public class ViewSetupWrapper extends BasicViewSetup
{
diff --git a/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java b/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java
index 570bf817afe5d581ea80230dc07b7c43eddff7ca..de05de48fe97165473e02a19f341bca5c5c0fe93 100644
--- a/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/FusionImageLoader.java
@@ -7,6 +7,7 @@ import io.scif.img.ImgOpener;
import java.util.HashMap;
import java.util.Map.Entry;
+import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
import mpicbg.spim.data.generic.sequence.ImgLoaderHint;
import mpicbg.spim.data.sequence.FinalVoxelDimensions;
import mpicbg.spim.data.sequence.ImgLoader;
@@ -35,15 +36,15 @@ import net.imglib2.view.Views;
* This {@link ImgLoader} loads images that represent a 3D stack as a sequence
* of slice with one image file per slice, such as created by Stephan
* Preibisch's Multi-view fusion plugin. It is constructed with the pattern of
- * the image filenames. Then, to laod the image for a given {@link ViewDescription}, its
- * TODO timepoint? index?, channel, and slice indices are filled into the
- * template to get the slice filenames.
+ * the image filenames. Then, to laod the image for a given
+ * {@link ViewDescription}, its TODO timepoint? index?, channel, and slice
+ * indices are filled into the template to get the slice filenames.
*
* This {@link ImgLoader} is used for exporting spim sequences to hdf5. Only the
- * {@link #getImage(ViewDescription)} method is implemented because this is
- * the only method required for exporting to hdf5.
+ * {@link BasicSetupImgLoader#getImage(int, ImgLoaderHint...)} method is
+ * implemented because this is the only method required for exporting to hdf5.
*
- * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
public class FusionImageLoader< T extends RealType< T > > implements ImgLoader
{
@@ -201,6 +202,5 @@ public class FusionImageLoader< T extends RealType< T > > implements ImgLoader
{
return new FinalVoxelDimensions( "px", 1, 1, 1 );
}
-
}
}
diff --git a/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java b/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java
index c37422f589491c3d27f1aa54563cf8c9c8344d54..2cbc55dc430cb439f34111b3fafa94a3ff43d916 100644
--- a/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/HuiskenImageLoader.java
@@ -24,7 +24,7 @@ import spimopener.SPIMExperiment;
* <a href="http://fiji.sc/javadoc/spimopener/package-summary.html">spimopener</a>
* to load images in Jan Husiken's format.
*
- * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
public class HuiskenImageLoader implements BasicImgLoader
{
diff --git a/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java b/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java
index c8072ef86c14368e41ec5f59894671ff81de84c9..01f80652ca3d80aee18d609ad2bf6e7ed4c058d8 100644
--- a/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/ImagePlusImgLoader.java
@@ -8,7 +8,6 @@ import mpicbg.spim.data.generic.sequence.BasicImgLoader;
import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
import mpicbg.spim.data.generic.sequence.ImgLoaderHint;
import mpicbg.spim.data.generic.sequence.TypedBasicImgLoader;
-import mpicbg.spim.data.sequence.ViewId;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.algorithm.stats.ComputeMinMax;
import net.imglib2.converter.Converter;
@@ -31,11 +30,12 @@ import bdv.img.virtualstack.VirtualStackImageLoader;
* Internally it relies on {@link VirtualStackImageLoader} to be able to handle
* large virtual stacks.
*
- * When {@link #getImage(ViewId) loading images}, the provided setup id is used
- * as the channel index of the {@link ImagePlus}, the provided timepoint id is
- * used as the frame index of the {@link ImagePlus}.
+ * When loading images ({@link #getSetupImgLoader(int)},
+ * {@link BasicSetupImgLoader#getImage(int, ImgLoaderHint...)}) the provided
+ * setup id is used as the channel index of the {@link ImagePlus}, the provided
+ * timepoint id is used as the frame index of the {@link ImagePlus}.
*
- * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
public class ImagePlusImgLoader< T extends Type< T > > implements TypedBasicImgLoader< T >
{
diff --git a/src/main/java/bdv/ij/export/imgloader/LegacyStackImageLoader.java b/src/main/java/bdv/ij/export/imgloader/LegacyStackImageLoader.java
index 9780c2fc386ae99cc226a4439cd91a467a34c250..954547fccac16c0e60e81ceef0f997c6d669017d 100644
--- a/src/main/java/bdv/ij/export/imgloader/LegacyStackImageLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/LegacyStackImageLoader.java
@@ -33,7 +33,7 @@ import org.scijava.app.StatusService;
* image for a given {@link ViewDescription}, its index in the filename list is computed as
* <code>view.getSetupIndex() + numViewSetups * view.getTimepointIndex()</code>.
*
- * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
public class LegacyStackImageLoader implements LegacyBasicImgLoader< UnsignedShortType >
{
diff --git a/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java b/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java
index d7dfda1d8ab805f2f494a8c41c510e1158af7a70..e73e7dc90c012b6e6cdef6d7aea11ace53a3a766 100644
--- a/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java
+++ b/src/main/java/bdv/ij/export/imgloader/StackImageLoader.java
@@ -16,7 +16,7 @@ import net.imglib2.type.numeric.integer.UnsignedShortType;
* image for a given {@link ViewDescription}, its index in the filename list is computed as
* <code>view.getSetupIndex() + numViewSetups * view.getTimepointIndex()</code>.
*
- * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
public class StackImageLoader extends LegacyBasicImgLoaderWrapper< UnsignedShortType, LegacyStackImageLoader >
{
diff --git a/src/main/java/bdv/ij/util/ProgressWriterIJ.java b/src/main/java/bdv/ij/util/ProgressWriterIJ.java
index 2e1fe42e1df61ca4387e8e89083e9cdac6008386..e5377943103fc07b115f43f7d9bb8b4826c9289e 100644
--- a/src/main/java/bdv/ij/util/ProgressWriterIJ.java
+++ b/src/main/java/bdv/ij/util/ProgressWriterIJ.java
@@ -36,4 +36,4 @@ public class ProgressWriterIJ implements ProgressWriter
{
IJ.showProgress( completionRatio );
}
-}
\ No newline at end of file
+}
diff --git a/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java b/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java
index a08e42d06f81d76e282f80d3bfab890deeae0ea8..9edcce0d48479748a876274a520ae38529d4e8b0 100644
--- a/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java
+++ b/src/main/java/bdv/img/imagestack/ImageStackImageLoader.java
@@ -157,4 +157,4 @@ public abstract class ImageStackImageLoader< T extends NumericType< T > & Native
{
return setupImgLoaders.get( setupId );
}
-}
\ No newline at end of file
+}
diff --git a/src/main/java/bdv/img/virtualstack/VirtualStackImageLoader.java b/src/main/java/bdv/img/virtualstack/VirtualStackImageLoader.java
index cf70983bceba6781b0b417543a651355a94a51f7..c103ff3c232b064ca551cff444b410dd0f282c71 100644
--- a/src/main/java/bdv/img/virtualstack/VirtualStackImageLoader.java
+++ b/src/main/java/bdv/img/virtualstack/VirtualStackImageLoader.java
@@ -4,6 +4,7 @@ import ij.ImagePlus;
import java.util.ArrayList;
+import mpicbg.spim.data.generic.sequence.BasicSetupImgLoader;
import mpicbg.spim.data.generic.sequence.ImgLoaderHint;
import mpicbg.spim.data.generic.sequence.TypedBasicImgLoader;
import mpicbg.spim.data.sequence.ViewId;
@@ -46,9 +47,10 @@ import bdv.img.cache.VolatileImgCells.CellCache;
* {@link #createUnsignedShortInstance(ImagePlus)} depending on the ImagePlus
* pixel type.
*
- * When {@link #getImage(ViewId) loading images}, the provided setup id is used
- * as the channel index of the {@link ImagePlus}, the provided timepoint id is
- * used as the frame index of the {@link ImagePlus}.
+ * When loading images ({@link #getSetupImgLoader(int)},
+ * {@link BasicSetupImgLoader#getImage(int, ImgLoaderHint...)}) the provided
+ * setup id is used as the channel index of the {@link ImagePlus}, the provided
+ * timepoint id is used as the frame index of the {@link ImagePlus}.
*
* @param <T>
* (non-volatile) pixel type
@@ -57,7 +59,7 @@ import bdv.img.cache.VolatileImgCells.CellCache;
* @param <A>
* volatile array access type
*
- * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
+ * @author Tobias Pietzsch <tobias.pietzsch@gmail.com>
*/
public abstract class VirtualStackImageLoader< T extends NativeType< T >, V extends Volatile< T > & NativeType< V >, A extends VolatileAccess >
implements ViewerImgLoader, TypedBasicImgLoader< T >