renamed everything N5 api related to N5Api

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

@@ -103,7 +103,7 @@
 import net.preibisch.mvrecon.fiji.plugin.Apply_Transformation;
 import net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5;
 import net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5;
-import net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5;
+import net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api;
 import net.preibisch.mvrecon.fiji.plugin.resave.PluginHelper;
 import net.preibisch.mvrecon.fiji.plugin.resave.ProgressWriterIJ;
 import net.preibisch.mvrecon.fiji.plugin.resave.Resave_HDF5;
@@ -1307,7 +1307,7 @@ else if (resaveAsN5)
 
 			IOFunctions.println( "N5 path: " + n5DatasetURI );
 
-			final ParametersResaveN5 n5params = ParametersResaveN5.getParamtersIJ(
+			final ParametersResaveN5Api n5params = ParametersResaveN5Api.getParamtersIJ(
 					xmlURI,
 					n5DatasetURI,
 					viewIds.stream().map( vid -> sd.getViewSetups().get( vid.getViewSetupId() ) ).collect( Collectors.toSet() ),

src/main/java/net/preibisch/mvrecon/fiji/plugin/fusion/DeconvolutionGUI.java

@@ -75,7 +75,7 @@
 import net.preibisch.mvrecon.process.deconvolution.iteration.sequential.ComputeBlockSeqThreadCUDAFactory;
 import net.preibisch.mvrecon.process.downsampling.DownsampleTools;
 import net.preibisch.mvrecon.process.export.DisplayImage;
-import net.preibisch.mvrecon.process.export.ExportN5API;
+import net.preibisch.mvrecon.process.export.ExportN5Api;
 import net.preibisch.mvrecon.process.export.ImgExport;
 import net.preibisch.mvrecon.process.export.Save3dTIFF;
 import net.preibisch.mvrecon.process.fusion.FusionTools;
@@ -95,7 +95,7 @@ public class DeconvolutionGUI implements FusionExportInterface
 
 		staticImgExportAlgorithms.add( new DisplayImage() );
 		staticImgExportAlgorithms.add( new Save3dTIFF( null ) );
-		staticImgExportAlgorithms.add( new ExportN5API() );
+		staticImgExportAlgorithms.add( new ExportN5Api() );
 
 		imgExportDescriptions = new String[ staticImgExportAlgorithms.size() ];
 

src/main/java/net/preibisch/mvrecon/fiji/plugin/fusion/FusionGUI.java

@@ -59,7 +59,7 @@
 import net.preibisch.mvrecon.process.downsampling.DownsampleTools;
 import net.preibisch.mvrecon.process.export.DisplayImage;
 import net.preibisch.mvrecon.process.export.ExportLarge2DTIFF;
-import net.preibisch.mvrecon.process.export.ExportN5API;
+import net.preibisch.mvrecon.process.export.ExportN5Api;
 import net.preibisch.mvrecon.process.export.ImgExport;
 import net.preibisch.mvrecon.process.export.OpenSeaDragon;
 import net.preibisch.mvrecon.process.export.Save3dTIFF;
@@ -128,7 +128,7 @@ public enum FusionType { AVG, AVG_BLEND, AVG_CONTENT, AVG_BLEND_CONTENT, MAX, FI
 
 		staticImgExportAlgorithms.add( new DisplayImage() );
 		staticImgExportAlgorithms.add( new Save3dTIFF( null ) );
-		staticImgExportAlgorithms.add( new ExportN5API() );
+		staticImgExportAlgorithms.add( new ExportN5Api() );
 		staticImgExportAlgorithms.add( new OpenSeaDragon() );
 
 		staticImgExportAlgorithms.add( new ExportLarge2DTIFF() );

src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/ParametersResaveN5.java → src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/ParametersResaveN5Api.java

@@ -46,7 +46,7 @@
 import net.preibisch.legacy.io.IOFunctions;
 import net.preibisch.mvrecon.fiji.plugin.util.GUIHelper;
 
-public class ParametersResaveN5
+public class ParametersResaveN5Api
 {
 	public static String[] compressions = new String[]{ "Bzip2", "Gzip", "Lz4", "Raw (no compression)", "Xz" };
 	public static int defaultBlockSize = 64;
@@ -69,13 +69,13 @@ public static URI createN5URIfromXMLURI( final URI xmlURI )
 		return URI.create( xmlURI.toString().subSequence( 0, xmlURI.toString().length() - 4 ) + ".n5" );
 	}
 
-	public static ParametersResaveN5 getParamtersIJ(
+	public static ParametersResaveN5Api getParamtersIJ(
 			final Collection< ViewSetup > setupsToProcess )
 	{
 		return getParamtersIJ( null, null, setupsToProcess, false );
 	}
 
-	public static ParametersResaveN5 getParamtersIJ(
+	public static ParametersResaveN5Api getParamtersIJ(
 			final URI xmlURI,
 			final Collection< ViewSetup > setupsToProcess,
 			final boolean askForPaths )
@@ -85,13 +85,13 @@ public static ParametersResaveN5 getParamtersIJ(
 		return getParamtersIJ( xmlURI, n5URI, setupsToProcess, askForPaths );
 	}
 
-	public static ParametersResaveN5 getParamtersIJ(
+	public static ParametersResaveN5Api getParamtersIJ(
 			final URI xmlURI,
 			final URI n5URI,
 			final Collection< ViewSetup > setupsToProcess,
 			final boolean askForPaths )
 	{
-		final ParametersResaveN5 n5params = new ParametersResaveN5();
+		final ParametersResaveN5Api n5params = new ParametersResaveN5Api();
 
 		final Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo = Resave_HDF5.proposeMipmaps( setupsToProcess ); //xml.getViewSetupsToProcess() );
 		final int firstviewSetupId = setupsToProcess.iterator().next().getId();// xml.getData().getSequenceDescription().getViewSetupsOrdered().get( 0 ).getId();
@@ -101,9 +101,9 @@ public static ParametersResaveN5 getParamtersIJ(
 		for ( final int[] row : autoMipmapSettings.getSubdivisions() )
 		{
 			Arrays.fill( row, defaultBlockSize );
-			row[ 0 ] = ParametersResaveN5.defaultBlockSizeXY;
+			row[ 0 ] = ParametersResaveN5Api.defaultBlockSizeXY;
 			if ( row.length >= 2 )
-				row[ 1 ] = ParametersResaveN5.defaultBlockSizeXY;
+				row[ 1 ] = ParametersResaveN5Api.defaultBlockSizeXY;
 		}
 
 		final long[] maxDimensions = setupsToProcess.iterator().next().getSize().dimensionsAsLongArray();

src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_N5Api.java

@@ -53,7 +53,7 @@
 import net.preibisch.mvrecon.fiji.plugin.queryXML.LoadParseQueryXML;
 import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
 import net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2;
-import net.preibisch.mvrecon.process.export.ExportN5API.StorageType;
+import net.preibisch.mvrecon.process.export.ExportN5Api.StorageType;
 import net.preibisch.mvrecon.process.n5api.N5ApiTools;
 import net.preibisch.mvrecon.process.n5api.N5ApiTools.MultiResolutionLevelInfo;
 import net.preibisch.mvrecon.process.n5api.SpimData2Tools;
@@ -70,7 +70,7 @@ public void run(String arg)
 		if ( !xml.queryXML( "Resaving as N5", "Resave", true, true, true, true, true ) )
 			return;
 
-		final ParametersResaveN5 n5params = ParametersResaveN5.getParamtersIJ( xml.getXMLURI(), xml.getViewSetupsToProcess(), true );
+		final ParametersResaveN5Api n5params = ParametersResaveN5Api.getParamtersIJ( xml.getXMLURI(), xml.getViewSetupsToProcess(), true );
 
 		if ( n5params == null )
 			return;
@@ -87,7 +87,7 @@ public void run(String arg)
 	public static SpimData2 resaveN5(
 			final SpimData2 data,
 			final Collection<? extends ViewId> vidsToResave,
-			final ParametersResaveN5 n5Params,
+			final ParametersResaveN5Api n5Params,
 			final boolean saveXML )
 	{
 		final SpimData2 sdReduced = SpimData2Tools.reduceSpimData2( data, vidsToResave.stream().collect( Collectors.toList() ) );
@@ -106,10 +106,10 @@ public static SpimData2 resaveN5(
 				ExportMipmapInfo exportMipmapInfo = n5Params.proposedMipmaps.get( k );
 				for (int[] row : exportMipmapInfo.getSubdivisions())
 				{
-					Arrays.fill( row, ParametersResaveN5.defaultBlockSize );
-					row[ 0 ] = ParametersResaveN5.defaultBlockSizeXY;
+					Arrays.fill( row, ParametersResaveN5Api.defaultBlockSize );
+					row[ 0 ] = ParametersResaveN5Api.defaultBlockSizeXY;
 					if ( row.length >= 2 )
-						row[ 1 ] = ParametersResaveN5.defaultBlockSizeXY;
+						row[ 1 ] = ParametersResaveN5Api.defaultBlockSizeXY;
 				}
 			});
 		}

src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java

@@ -42,7 +42,7 @@
 import mpicbg.spim.data.sequence.ViewSetup;
 import net.preibisch.legacy.io.IOFunctions;
 import net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5;
-import net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5;
+import net.preibisch.mvrecon.fiji.plugin.resave.ParametersResaveN5Api;
 import net.preibisch.mvrecon.fiji.plugin.resave.ProgressWriterIJ;
 import net.preibisch.mvrecon.fiji.plugin.resave.Resave_HDF5;
 import net.preibisch.mvrecon.fiji.plugin.resave.Resave_N5Api;
@@ -286,9 +286,9 @@ else if (index == 4 || index == 5) // 4 == in-place, 5 == choose path
 					{
 						panel.saveXML();
 
-						final URI n5DatasetURI = ParametersResaveN5.createN5URIfromXMLURI( panel.xml() );
+						final URI n5DatasetURI = ParametersResaveN5Api.createN5URIfromXMLURI( panel.xml() );
 
-						final ParametersResaveN5 n5params = ParametersResaveN5.getParamtersIJ(
+						final ParametersResaveN5Api n5params = ParametersResaveN5Api.getParamtersIJ(
 								panel.xml(),
 								n5DatasetURI,
 								viewIds.stream().map( vid -> data.getSequenceDescription().getViewSetups().get( vid.getViewSetupId() ) ).collect( Collectors.toSet() ),

src/main/java/net/preibisch/mvrecon/process/export/DisplayImage.java

@@ -197,7 +197,7 @@ public boolean queryParameters( final FusionExportInterface fusion )
 		gd.addNumericField( "min_intensity", defaultMinIntensity, 0);
 		gd.addNumericField( "max_intensity", defaultMaxIntensity, 0);
 
-		gd.addCheckbox( "Show_advanced_block_size_options (in a new dialog, can optimize processing time)", ExportN5API.defaultAdvancedBlockSize );
+		gd.addCheckbox( "Show_advanced_block_size_options (in a new dialog, can optimize processing time)", ExportN5Api.defaultAdvancedBlockSize );
 
 		if ( is2d )
 			gd.addMessage( "Note: we have a 2d-dataset, choose 1 in z.", GUIHelper.smallStatusFont, GUIHelper.neutral );
@@ -214,7 +214,7 @@ public boolean queryParameters( final FusionExportInterface fusion )
 		minIntensity = defaultMinIntensity = (int)Math.round( gd.getNextNumber() );
 		maxIntensity = defaultMaxIntensity = (int)Math.round( gd.getNextNumber() );
 
-		if ( ExportN5API.defaultAdvancedBlockSize  = gd.getNextBoolean() )
+		if ( ExportN5Api.defaultAdvancedBlockSize  = gd.getNextBoolean() )
 		{
 			final GenericDialog gd2 = new GenericDialog( "Compute block size options" );
 

src/main/java/net/preibisch/mvrecon/process/export/ExportN5API.java

@@ -81,7 +81,7 @@
 import util.Grid;
 import util.URITools;
 
-public class ExportN5API implements ImgExport
+public class ExportN5Api implements ImgExport
 {
 	public enum StorageType { N5, ZARR, HDF5 }
 
@@ -156,7 +156,7 @@ public boolean finish()
 	public int[] computeBlocksizeFactor() { return new int[] { bsFactorX, bsFactorY, bsFactorZ }; }
 
 	@Override
-	public ImgExport newInstance() { return new ExportN5API(); }
+	public ImgExport newInstance() { return new ExportN5Api(); }
 
 	@Override
 	public String getDescription() { return "ZARR/N5/HDF5 export using N5-API"; }

src/main/java/net/preibisch/mvrecon/process/n5api/N5ApiTools.java

@@ -40,7 +40,7 @@
 import net.preibisch.legacy.io.IOFunctions;
 import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
 import net.preibisch.mvrecon.process.downsampling.lazy.LazyHalfPixelDownsample2x;
-import net.preibisch.mvrecon.process.export.ExportN5API.StorageType;
+import net.preibisch.mvrecon.process.export.ExportN5Api.StorageType;
 import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
 import util.Grid;
 

src/main/java/net/preibisch/mvrecon/process/n5api/SpimData2Tools.java

@@ -56,7 +56,7 @@
 import net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPoints;
 import net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunctions;
 import net.preibisch.mvrecon.fiji.spimdata.stitchingresults.StitchingResults;
-import net.preibisch.mvrecon.process.export.ExportN5API.StorageType;
+import net.preibisch.mvrecon.process.export.ExportN5Api.StorageType;
 import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
 import net.preibisch.mvrecon.process.n5api.N5ApiTools.MultiResolutionLevelInfo;
 import util.URITools;