consolidated all helper methods in two classes N5ApiTools.java and Sp…

…imData2Tools.java
PreibischLab · Sep 11, 2024 · 287d813 · 287d813
1 parent 37be616
commit 287d813
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Showing 9 changed files with 961 additions and 1,221 deletions.
diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_HDF5.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_HDF5.java
@@ -47,7 +47,7 @@
 import net.preibisch.mvrecon.fiji.plugin.resave.Generic_Resave_HDF5.ParametersResaveHDF5;
 import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
 import net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2;
-import net.preibisch.mvrecon.process.resave.SpimData2Tools;
+import net.preibisch.mvrecon.process.n5api.SpimData2Tools;
 
 public class Resave_HDF5 implements PlugIn
 {

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_N5.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_N5.java
@@ -51,10 +51,9 @@
 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.ExportTools;
-import net.preibisch.mvrecon.process.export.ExportTools.MultiResolutionLevelInfo;
-import net.preibisch.mvrecon.process.resave.N5ResaveTools;
-import net.preibisch.mvrecon.process.resave.SpimData2Tools;
+import net.preibisch.mvrecon.process.n5api.N5ApiTools;
+import net.preibisch.mvrecon.process.n5api.SpimData2Tools;
+import net.preibisch.mvrecon.process.n5api.N5ApiTools.MultiResolutionLevelInfo;
 import util.Grid;
 import util.URITools;
 
@@ -123,24 +122,24 @@ public static SpimData2 resaveN5(
 			computeBlockSize[ d ] = blockSize[ d ] * n5Params.blockSizeFactor[ d ];
 
 		final HashMap<Integer, long[]> dimensions =
-				N5ResaveTools.assembleDimensions( data, vidsToResave );
+				N5ApiTools.assembleDimensions( data, vidsToResave );
 
 		final int[][] downsamplings =
-				N5ResaveTools.mipMapInfoToDownsamplings( n5Params.proposedMipmaps );
+				N5ApiTools.mipMapInfoToDownsamplings( n5Params.proposedMipmaps );
 
 		final ArrayList<long[][]> grid =
-				N5ResaveTools.assembleS0Jobs( vidsToResave, dimensions, blockSize, computeBlockSize );
+				N5ApiTools.assembleS0Jobs( vidsToResave, dimensions, blockSize, computeBlockSize );
 
 		final Map<Integer, DataType> dataTypes =
-				N5ResaveTools.assembleDataTypes( data, dimensions.keySet() );
+				N5ApiTools.assembleDataTypes( data, dimensions.keySet() );
 
 		// create all datasets and write BDV metadata for all ViewIds (including downsampling)
 		final HashMap< ViewId, MultiResolutionLevelInfo[] > viewIdToMrInfo = new HashMap<>();
 
 		long time = System.currentTimeMillis();
 
 		for ( final ViewId viewId : vidsToResave )
-			viewIdToMrInfo.put( viewId , ExportTools.setupBdvDatasetsN5(
+			viewIdToMrInfo.put( viewId , N5ApiTools.setupBdvDatasetsN5(
 				n5Writer, viewId,
 				dataTypes.get( viewId.getViewSetupId() ),
 				dimensions.get( viewId.getViewSetupId() ),
@@ -164,11 +163,11 @@ public static SpimData2 resaveN5(
 		try
 		{
 			myPool.submit(() -> grid.parallelStream().forEach(
-					gridBlock -> N5ResaveTools.resaveS0Block(
+					gridBlock -> N5ApiTools.resaveS0Block(
 							data,
 							n5Writer,
-							dataTypes.get( N5ResaveTools.gridBlockToViewId( gridBlock ).getViewSetupId() ),
-							N5ResaveTools.gridToDatasetBdv( 0, StorageType.N5 ), // a function mapping the gridblock to the dataset name for level 0 and N5
+							dataTypes.get( N5ApiTools.gridBlockToViewId( gridBlock ).getViewSetupId() ),
+							N5ApiTools.gridToDatasetBdv( 0, StorageType.N5 ), // a function mapping the gridblock to the dataset name for level 0 and N5
 							gridBlock ) ) ).get();
 		}
 		catch (InterruptedException | ExecutionException e)
@@ -186,9 +185,9 @@ public static SpimData2 resaveN5(
 		for ( int level = 1; level < downsamplings.length; ++level )
 		{
 			final int s = level;
-			final int[] ds = N5ResaveTools.computeRelativeDownsampling( downsamplings, s );
+			final int[] ds = N5ApiTools.computeRelativeDownsampling( downsamplings, s );
 			final ArrayList<long[][]> allBlocks =
-					N5ResaveTools.assembleDownsamplingJobs( vidsToResave, viewIdToMrInfo, level );
+					N5ApiTools.assembleDownsamplingJobs( vidsToResave, viewIdToMrInfo, level );
 
 			IOFunctions.println( "Downsampling: " + Util.printCoordinates( downsamplings[ s ] ) + " with relative downsampling of " + Util.printCoordinates( ds ));
 			IOFunctions.println( "Number of compute blocks: " + allBlocks.size() );
@@ -200,10 +199,10 @@ public static SpimData2 resaveN5(
 				myPool.submit(() -> allBlocks.parallelStream().forEach(
 						gridBlock -> 
 						{
-							N5ResaveTools.writeDownsampledBlock(
+							N5ApiTools.writeDownsampledBlock(
 								n5Writer,
-								viewIdToMrInfo.get( N5ResaveTools.gridBlockToViewId( gridBlock ) )[ s ], //N5ResaveTools.gridToDatasetBdv( s, StorageType.N5 ),
-								viewIdToMrInfo.get( N5ResaveTools.gridBlockToViewId( gridBlock ) )[ s - 1 ],//N5ResaveTools.gridToDatasetBdv( s - 1, StorageType.N5 ),
+								viewIdToMrInfo.get( N5ApiTools.gridBlockToViewId( gridBlock ) )[ s ], //N5ResaveTools.gridToDatasetBdv( s, StorageType.N5 ),
+								viewIdToMrInfo.get( N5ApiTools.gridBlockToViewId( gridBlock ) )[ s - 1 ],//N5ResaveTools.gridToDatasetBdv( s - 1, StorageType.N5 ),
 								gridBlock );
 						} ) ).get();
 			}

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_TIFF.java b/src/main/java/net/preibisch/mvrecon/fiji/plugin/resave/Resave_TIFF.java
@@ -43,7 +43,7 @@
 import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
 import net.preibisch.mvrecon.fiji.spimdata.imgloaders.StackImgLoaderIJ;
 import net.preibisch.mvrecon.process.export.Save3dTIFF;
-import net.preibisch.mvrecon.process.resave.SpimData2Tools;
+import net.preibisch.mvrecon.process.n5api.SpimData2Tools;
 import util.URITools;
 
 public class Resave_TIFF implements PlugIn

diff --git a/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java b/src/main/java/net/preibisch/mvrecon/fiji/spimdata/explorer/popup/ResavePopup.java
@@ -52,7 +52,7 @@
 import net.preibisch.mvrecon.fiji.spimdata.explorer.ExplorerWindow;
 import net.preibisch.mvrecon.fiji.spimdata.explorer.FilteredAndGroupedExplorerPanel;
 import net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPointLists;
-import net.preibisch.mvrecon.process.resave.SpimData2Tools;
+import net.preibisch.mvrecon.process.n5api.SpimData2Tools;
 import util.URITools;
 
 public class ResavePopup extends JMenu implements ExplorerWindowSetable

diff --git a/src/main/java/net/preibisch/mvrecon/process/export/ExportN5API.java b/src/main/java/net/preibisch/mvrecon/process/export/ExportN5API.java
@@ -65,9 +65,10 @@
 import net.preibisch.mvrecon.fiji.plugin.resave.PluginHelper;
 import net.preibisch.mvrecon.fiji.plugin.util.GUIHelper;
 import net.preibisch.mvrecon.process.deconvolution.DeconViews;
-import net.preibisch.mvrecon.process.export.ExportTools.InstantiateViewSetupBigStitcher;
 import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
-import net.preibisch.mvrecon.process.resave.N5ResaveTools;
+import net.preibisch.mvrecon.process.n5api.N5ApiTools;
+import net.preibisch.mvrecon.process.n5api.SpimData2Tools;
+import net.preibisch.mvrecon.process.n5api.SpimData2Tools.InstantiateViewSetupBigStitcher;
 import util.Grid;
 import util.URITools;
 
@@ -225,7 +226,7 @@ else if ( FloatType.class.isInstance( type ) )
 
 			IOFunctions.println( "Assigning ViewId " + Group.pvid( viewId ) );
 
-			dataset = ExportTools.createBDVPath( viewId, 0, this.storageType );
+			dataset = N5ApiTools.createBDVPath( viewId, 0, this.storageType );
 		}
 
 		//
@@ -264,7 +265,7 @@ else if ( FloatType.class.isInstance( type ) )
 			try
 			{
 				// the first time the XML does not exist, thus instantiate is not called
-				if ( ExportTools.writeBDVMetaData(
+				if ( SpimData2Tools.writeBDVMetaData(
 						driverVolumeWriter,
 						storageType,
 						dataType,
@@ -359,7 +360,7 @@ else if ( FloatType.class.isInstance( type ) )
 			for ( int level = 1; level < this.downsampling.length; ++level )
 			{
 				final int s = level;
-				final int[] ds = N5ResaveTools.computeRelativeDownsampling( this.downsampling, level );
+				final int[] ds = N5ApiTools.computeRelativeDownsampling( this.downsampling, level );
 
 				IOFunctions.println( "Downsampling: " + Util.printCoordinates( this.downsampling[ level ] ) + " with relative downsampling of " + Util.printCoordinates( ds ));
 
@@ -368,7 +369,7 @@ else if ( FloatType.class.isInstance( type ) )
 					dim[ d ] = previousDim[ d ] / ds[ d ];
 
 				final String datasetDownsampling = bdv ?
-								ExportTools.createDownsampledBDVPath(dataset, level, storageType) : dataset.substring(0, dataset.length() - 3) + "/s" + level;
+						N5ApiTools.createDownsampledBDVPath(dataset, level, storageType) : dataset.substring(0, dataset.length() - 3) + "/s" + level;
 
 				try
 				{
@@ -400,7 +401,7 @@ else if ( FloatType.class.isInstance( type ) )
 				final Function<long[][], String> gridBlockToDatasetPreviousScale = (gridBlock -> datasetPrev); // there is only one ViewId
 
 				e.submit( () -> gridDS.parallelStream().forEach(
-						gridBlock -> N5ResaveTools.writeDownsampledBlock(
+						gridBlock -> N5ApiTools.writeDownsampledBlock(
 								driverVolumeWriter,
 								gridBlockToDataset,
 								gridBlockToDatasetPreviousScale,