Merge branch 'PreibischLab:master' into master

LICENSE.txt

@@ -1,12 +1,12 @@
-		    GNU GENERAL PUBLIC LICENSE
-		       Version 2, June 1991
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
 
  Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
  Everyone is permitted to copy and distribute verbatim copies
  of this license document, but changing it is not allowed.
 
-			    Preamble
+                            Preamble
 
   The licenses for most software are designed to take away your
 freedom to share and change it.  By contrast, the GNU General Public
@@ -56,7 +56,7 @@ patent must be licensed for everyone's free use or not licensed at all.
   The precise terms and conditions for copying, distribution and
 modification follow.
 
-		    GNU GENERAL PUBLIC LICENSE
+                    GNU GENERAL PUBLIC LICENSE
    TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
 
   0. This License applies to any program or other work which contains
@@ -255,7 +255,7 @@ make exceptions for this.  Our decision will be guided by the two goals
 of preserving the free status of all derivatives of our free software and
 of promoting the sharing and reuse of software generally.
 
-			    NO WARRANTY
+                            NO WARRANTY
 
   11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
 FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
@@ -277,9 +277,9 @@ YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
 PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGES.
 
-		     END OF TERMS AND CONDITIONS
+                     END OF TERMS AND CONDITIONS
 
-	    How to Apply These Terms to Your New Programs
+            How to Apply These Terms to Your New Programs
 
   If you develop a new program, and you want it to be of the greatest
 possible use to the public, the best way to achieve this is to make it

pom.xml

@@ -5,13 +5,13 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>33.2.0</version>
+		<version>36.0.0</version>
 		<relativePath />
 	</parent>
 
 	<groupId>net.preibisch</groupId>
 	<artifactId>multiview-reconstruction</artifactId>
-	<version>1.2.9-SNAPSHOT</version>
+	<version>3.2.4-SNAPSHOT</version>
 
 	<name>Multiview Reconstruction</name>
 	<description>Software for the reconstruction of multi-view microscopic acquisitions
@@ -99,10 +99,18 @@ like Selective Plane Illumination Microscopy (SPIM) Data.</description>
 		<license.licenseName>gpl_v2</license.licenseName>
 		<license.copyrightOwners>Multiview Reconstruction developers.</license.copyrightOwners>
 
-		<multiview-simulation.version>0.2.0</multiview-simulation.version>
+		<pyramidio.version>1.1.0</pyramidio.version>
+		<ijp-kheops.version>0.3.4</ijp-kheops.version>
 
 		<!-- NB: Deploy releases to the SciJava Maven repository. -->
 		<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>
+
+		<imglib2.version>6.1.0</imglib2.version>
+		<imglib2-algorithm.version>0.13.2</imglib2-algorithm.version>
+		<imglib2-cache.version>1.0.0-beta-17</imglib2-cache.version>
+		<bigdataviewer-core.version>10.4.6</bigdataviewer-core.version>
+		<bigdataviewer-vistools.version>1.0.0-beta-32</bigdataviewer-vistools.version>
+		<n5-imglib2.version>5.0.0</n5-imglib2.version>
 	</properties>
 
 	<repositories>
@@ -158,7 +166,6 @@ like Selective Plane Illumination Microscopy (SPIM) Data.</description>
 		<dependency>
 			<groupId>net.imglib2</groupId>
 			<artifactId>imglib2-algorithm</artifactId>
-			<version>0.13.0</version>
 		</dependency>
 		<dependency>
 			<groupId>net.imglib2</groupId>
@@ -241,7 +248,6 @@ like Selective Plane Illumination Microscopy (SPIM) Data.</description>
 		<dependency>
 			<groupId>args4j</groupId>
 			<artifactId>args4j</artifactId>
-			<version>2.33</version>
 		</dependency>
 		<dependency>
 			<groupId>org.janelia.saalfeldlab</groupId>
@@ -262,12 +268,16 @@ like Selective Plane Illumination Microscopy (SPIM) Data.</description>
 		<dependency>
 			<groupId>gov.nist.isg</groupId>
 			<artifactId>pyramidio</artifactId>
-			<version>1.1.0</version>
+			<version>${pyramidio.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>ch.epfl.biop</groupId>
 			<artifactId>ijp-kheops</artifactId>
-			<version>0.3.4</version>
+			<version>${ijp-kheops.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>info.picocli</groupId>
+			<artifactId>picocli</artifactId>
 		</dependency>
 	</dependencies>
 

src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/DHM.java

@@ -73,7 +73,7 @@ public String getExtendedDescription()
 	}
 
 	@Override
-	public SpimData2 createDataset()
+	public SpimData2 createDataset( final String xmlFileName )
 	{
 		final DHMMetaData meta = queryDirectoryAndRatio();
 
@@ -116,7 +116,7 @@ public SpimData2 createDataset()
 
 		// create the initial view interest point object
 		final ViewInterestPoints viewInterestPoints = new ViewInterestPoints();
-		viewInterestPoints.createViewInterestPoints( sequenceDescription.getViewDescriptions() );
+		//viewInterestPoints.createViewInterestPoints( sequenceDescription.getViewDescriptions() );
 
 		// finally create the SpimData itself based on the sequence description and the view registration
 		final SpimData2 spimData = new SpimData2( meta.getDir(), sequenceDescription, viewRegistrations, viewInterestPoints, new BoundingBoxes(), new PointSpreadFunctions(), new StitchingResults(), new IntensityAdjustments() );
@@ -207,6 +207,6 @@ public MultiViewDatasetDefinition newInstance()
 
 	public static void main( String[] args )
 	{
-		new DHM().createDataset();
+		new DHM().createDataset( "dataset.xml" );
 	}
 }

src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/FileListDatasetDefinition.java

@@ -124,11 +124,15 @@
 public class FileListDatasetDefinition implements MultiViewDatasetDefinition
 {
 	public static final String[] GLOB_SPECIAL_CHARS = new String[] {"{", "}", "[", "]", "*", "?"};
-	public static final String[] loadChoices = new String[] { "Re-save as multiresolution HDF5", "Re-save as multiresolution N5", "Load raw data virtually (with caching)", "Load raw data"};
+	//public static final String[] loadChoices = new String[] { "Re-save as multiresolution HDF5", "Re-save as multiresolution N5", "Load raw data virtually (with caching)", "Load raw data"};
+	public static final String[] loadChoicesNew = new String[] { "Re-save as multiresolution HDF5", "Re-save as multiresolution N5", "Load raw data directly"};
 	public static final String Z_VARIABLE_CHOICE = "Z-Planes (experimental)";
 
 	public static boolean windowsHack = true;
 
+	public static int defaultLoadChoice = 0;
+	public static boolean defaultVirtual = true;
+
 	private static ArrayList<FileListChooser> fileListChoosers = new ArrayList<>();
 	static
 	{
@@ -619,9 +623,9 @@ else if ( aInfoI.axis == 2 )
 
 		final ImgLoader imgLoader;
 		if (withVirtualLoader)
-			imgLoader = new FileMapImgLoaderLOCI2( fileMap, FileListDatasetDefinitionUtil.selectImgFactory(state.getDimensionMap()), sd, state.getWasZGrouped() );
+			imgLoader = new FileMapImgLoaderLOCI2( fileMap, sd, state.getWasZGrouped() );
 		else
-			imgLoader = new FileMapImgLoaderLOCI( fileMap, FileListDatasetDefinitionUtil.selectImgFactory(state.getDimensionMap()), sd, state.getWasZGrouped() );
+			imgLoader = new FileMapImgLoaderLOCI( fileMap, sd, state.getWasZGrouped() );
 		sd.setImgLoader( imgLoader );
 
 		double minResolution = Double.MAX_VALUE;
@@ -636,15 +640,15 @@ else if ( aInfoI.axis == 2 )
 
 		// create the initial view interest point object
 		final ViewInterestPoints viewInterestPoints = new ViewInterestPoints();
-		viewInterestPoints.createViewInterestPoints( sd.getViewDescriptions() );
+		//viewInterestPoints.createViewInterestPoints( sd.getViewDescriptions() );
 
 		SpimData2 data = new SpimData2( new File("/"), sd, vrs, viewInterestPoints, new BoundingBoxes(), new PointSpreadFunctions(), new StitchingResults(), new IntensityAdjustments() );
 		return data;
 	}
 
 
 	@Override
-	public SpimData2 createDataset( )
+	public SpimData2 createDataset( final String xmlFileName )
 	{
 
 		FileListChooser chooser = fileListChoosers.get( 0 );
@@ -1078,7 +1082,8 @@ else if (choice.equals( Z_VARIABLE_CHOICE ))
 		GenericDialogPlus gdSave = new GenericDialogPlus( "Save dataset definition" );
 
 		addMessageAsJLabel("<html> <h1> Loading options </h1> <br /> </html>", gdSave);
-		gdSave.addChoice( "how_to_load_images", loadChoices, loadChoices[0] );
+		gdSave.addChoice( "how_to_load_images", loadChoicesNew, loadChoicesNew[defaultLoadChoice] );
+		gdSave.addCheckbox( "load_raw_data_virtually (also when resaving to HDF5/N5, slower, but supports larger stacks)", defaultVirtual );
 
 		addMessageAsJLabel("<html><h2> Save path </h2></html>", gdSave);
 
@@ -1123,8 +1128,9 @@ else if (choice.equals( Z_VARIABLE_CHOICE ))
 		if ( gdSave.wasCanceled() )
 			return null;
 
-		final int loadChoice = gdSave.getNextChoiceIndex();
-		final boolean useVirtualLoader = loadChoice == 2; //"Re-save as multiresolution HDF5", "Re-save as multiresolution N5", "Load raw data virtually (with caching)", "Load raw data"
+		final int loadChoice = defaultLoadChoice = gdSave.getNextChoiceIndex();
+		final boolean useVirtualLoader = defaultVirtual = gdSave.getNextBoolean();
+
 		// re-build the SpimData if user explicitly doesn't want virtual loading
 		if (!useVirtualLoader)
 			data = buildSpimData( state, useVirtualLoader );
@@ -1196,20 +1202,23 @@ public int compare(Group< ViewDescription > o1, Group< ViewDescription > o2)
 		{
 			final Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo = Resave_HDF5.proposeMipmaps( data.getSequenceDescription().getViewSetupsOrdered() );
 			final int firstviewSetupId = data.getSequenceDescription().getViewSetupsOrdered().get( 0 ).getId();
-			Generic_Resave_HDF5.lastExportPath = String.join( File.separator, chosenPath.getAbsolutePath(), "dataset");
-			final Parameters params = Generic_Resave_HDF5.getParameters( perSetupExportMipmapInfo.get( firstviewSetupId ), true, true );
+			//Generic_Resave_HDF5.lastExportPath = String.join( File.separator, chosenPath.getAbsolutePath(), "dataset");
+			final Parameters params = Generic_Resave_HDF5.getParameters( perSetupExportMipmapInfo.get( firstviewSetupId ), false, true );
 
 			// HDF5 options dialog was cancelled
 			if (params == null)
 				return null;
 
+			params.setHDF5File(new File( chosenPath.getAbsolutePath(), xmlFileName.subSequence( 0, xmlFileName.length() - 4 ) + ".h5" ) );
+			params.setSeqFile(new File( chosenPath.getAbsolutePath(), xmlFileName ) );
+
 			final ProgressWriter progressWriter = new ProgressWriterIJ();
 			progressWriter.out().println( "starting export..." );
 
 			Generic_Resave_HDF5.writeHDF5( data, params, progressWriter );
-			
+
 			IOFunctions.println( "(" + new Date(  System.currentTimeMillis() ) + "): HDF5 resave finished." );
-			
+
 			net.preibisch.mvrecon.fiji.ImgLib2Temp.Pair< SpimData2, List< String > > result = Resave_HDF5.createXMLObject( data, new ArrayList<>(data.getSequenceDescription().getViewDescriptions().keySet()), params, progressWriter, true );
 
 			// ensure progressbar is gone
@@ -1224,7 +1233,7 @@ public int compare(Group< ViewDescription > o1, Group< ViewDescription > o2)
 			final ArrayList< ViewDescription > viewIds = new ArrayList<>( data.getSequenceDescription().getViewDescriptions().values() );
 			Collections.sort( viewIds );
 
-			final File xmlFile = new File( chosenPath.getAbsolutePath(), "dataset.xml" );
+			final File xmlFile = new File( chosenPath.getAbsolutePath(), xmlFileName );
 
 			final SequenceDescription sd = data.getSequenceDescription();
 
@@ -1236,7 +1245,8 @@ public int compare(Group< ViewDescription > o1, Group< ViewDescription > o2)
 			if ( n5params == null )
 				return null;
 
-			n5params.n5File =  new File( chosenPath.getAbsolutePath(), "dataset.n5" );
+			// n5-filename is same as XML name now (set in N5Parameters.getParamtersIJ)
+			//n5params.n5File =  new File( chosenPath.getAbsolutePath(), "dataset.n5" );
 
 			Resave_N5.resaveN5( data, viewIds, n5params );