add status bars for saving

PreibischLab · Sep 13, 2024 · c3295bb · c3295bb
1 parent 2dd834d
commit c3295bb
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Showing 2 changed files with 34 additions and 6 deletions.
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
@@ -32,6 +32,7 @@
 import java.util.concurrent.ExecutionException;
 import java.util.concurrent.ForkJoinPool;
 import java.util.concurrent.TimeUnit;
+import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Collectors;
 
 import org.janelia.saalfeldlab.n5.Compression;
@@ -41,6 +42,7 @@
 import bdv.export.ExportMipmapInfo;
 import bdv.export.ProgressWriter;
 import bdv.img.n5.N5ImageLoader;
+import ij.IJ;
 import ij.plugin.PlugIn;
 import mpicbg.spim.data.sequence.TimePoint;
 import mpicbg.spim.data.sequence.ViewId;
@@ -160,6 +162,9 @@ public static SpimData2 resaveN5(
 		IOFunctions.println( "Downsamplings: " + Arrays.deepToString( downsamplings ) );
 		IOFunctions.println( "Number of compute blocks: " + grid.size() );
 
+		final AtomicInteger progress = new AtomicInteger( 0 );
+		IJ.showProgress( progress.get(), grid.size() );
+
 		//
 		// Save full resolution dataset (s0)
 		//
@@ -170,12 +175,17 @@ public static SpimData2 resaveN5(
 		try
 		{
 			myPool.submit(() -> grid.parallelStream().forEach(
-					gridBlock -> N5ApiTools.resaveS0Block(
+					gridBlock -> 
+					{
+						N5ApiTools.resaveS0Block(
 							data,
 							n5Writer,
 							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();
+							gridBlock );
+
+						IJ.showProgress( progress.incrementAndGet(), grid.size() );
+					})).get();
 		}
 		catch (InterruptedException | ExecutionException e)
 		{
@@ -184,6 +194,7 @@ public static SpimData2 resaveN5(
 			return null;
 		}
 
+		IJ.showProgress( progress.getAndSet( 0 ), grid.size() );
 		IOFunctions.println( "Saved level s0, took: " + (System.currentTimeMillis() - time ) + " ms." );
 
 		//
@@ -192,8 +203,6 @@ public static SpimData2 resaveN5(
 		for ( int level = 1; level < downsamplings.length; ++level )
 		{
 			final int s = level;
-			//final ArrayList<long[][]> allBlocks =
-			//		N5ApiTools.assembleJobs( vidsToResave, viewIdToMrInfo, level );
 
 			final List<long[][]> allBlocks =
 					vidsToResave.stream().map( viewId ->
@@ -203,6 +212,7 @@ public static SpimData2 resaveN5(
 
 			IOFunctions.println( "Downsampling level s" + s + "... " );
 			IOFunctions.println( "Number of compute blocks: " + allBlocks.size() );
+			IJ.showProgress( progress.get(), allBlocks.size() );
 
 			time = System.currentTimeMillis();
 
@@ -216,6 +226,8 @@ public static SpimData2 resaveN5(
 								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 );
+
+							IJ.showProgress( progress.incrementAndGet(), allBlocks.size() );
 						} ) ).get();
 			}
 			catch (InterruptedException | ExecutionException e)
@@ -225,6 +237,7 @@ public static SpimData2 resaveN5(
 				return null;
 			}
 
+			IJ.showProgress( progress.getAndSet( 0 ), allBlocks.size() );
 			IOFunctions.println( "Resaved N5 s" + s + " level, took: " + (System.currentTimeMillis() - time ) + " ms." );
 		}
 

diff --git a/src/main/java/net/preibisch/mvrecon/process/export/ExportN5API.java b/src/main/java/net/preibisch/mvrecon/process/export/ExportN5API.java
@@ -34,6 +34,7 @@
 import java.util.concurrent.ExecutionException;
 import java.util.concurrent.ForkJoinPool;
 import java.util.concurrent.TimeUnit;
+import java.util.concurrent.atomic.AtomicInteger;
 
 import org.janelia.saalfeldlab.n5.Compression;
 import org.janelia.saalfeldlab.n5.DataType;
@@ -46,6 +47,7 @@
 import bdv.export.ExportMipmapInfo;
 import bdv.export.ProposeMipmaps;
 import fiji.util.gui.GenericDialogPlus;
+import ij.IJ;
 import ij.gui.GenericDialog;
 import mpicbg.spim.data.SpimDataException;
 import mpicbg.spim.data.generic.sequence.BasicViewSetup;
@@ -279,6 +281,9 @@ else if ( FloatType.class.isInstance( type ) )
 		IOFunctions.println( "num blocks = " + Grid.create( bb.dimensionsAsLongArray(), blocksize() ).size() + ", size = " + bsX + "x" + bsY + "x" + bsZ );
 		IOFunctions.println( "num compute blocks = " + grid.size() + ", size = " + bsX*bsFactorX + "x" + bsY*bsFactorY + "x" + bsZ*bsFactorZ );
 
+		final AtomicInteger progress = new AtomicInteger( 0 );
+		IJ.showProgress( progress.get(), grid.size() );
+
 		//
 		// save full-resolution data (s0)
 		//
@@ -304,6 +309,8 @@ else if ( FloatType.class.isInstance( type ) )
 
 								final RandomAccessibleInterval sourceGridBlock = Views.offsetInterval(source, gridBlock[0], gridBlock[1]);
 								N5Utils.saveBlock(sourceGridBlock, driverVolumeWriter, mrInfo[ 0 ].dataset, gridBlock[2]);
+
+								IJ.showProgress( progress.incrementAndGet(), grid.size() );
 							}
 							catch (Exception e) 
 							{
@@ -323,6 +330,7 @@ else if ( FloatType.class.isInstance( type ) )
 		}
 
 		//System.out.println( "Saved, e.g. view with './n5-view -i " + n5Path + " -d " + n5Dataset );
+		IJ.showProgress( progress.getAndSet( 0 ), grid.size() );
 		IOFunctions.println( new Date( System.currentTimeMillis() ) + ": Saved full resolution, took: " + (System.currentTimeMillis() - time ) + " ms." );
 
 		//
@@ -336,17 +344,23 @@ else if ( FloatType.class.isInstance( type ) )
 			IOFunctions.println( new Date( System.currentTimeMillis() ) + ": Downsampling: " + Util.printCoordinates( mrInfo[ level ].absoluteDownsampling ) + " with relative downsampling of " + Util.printCoordinates( mrInfo[ level ].relativeDownsampling ));
 			IOFunctions.println( new Date( System.currentTimeMillis() ) + ": s" + level + " num blocks=" + allBlocks.size() );
 			IOFunctions.println( new Date( System.currentTimeMillis() ) + ": Loading '" + mrInfo[ level - 1 ].dataset + "', downsampled will be written as '" + mrInfo[ level ].dataset + "'." );
+			IJ.showProgress( progress.get(), allBlocks.size() );
 
 			time = System.currentTimeMillis();
 
 			try
 			{
 				myPool.submit( () -> allBlocks.parallelStream().forEach(
-						gridBlock -> N5ApiTools.writeDownsampledBlock(
+						gridBlock ->
+						{
+							N5ApiTools.writeDownsampledBlock(
 								driverVolumeWriter,
 								mrInfo[ s ],
 								mrInfo[ s - 1 ],
-								gridBlock ) ) ).get();
+								gridBlock );
+
+							IJ.showProgress( progress.incrementAndGet(), allBlocks.size() );
+						})).get();
 
 				myPool.shutdown();
 				myPool.awaitTermination( Long.MAX_VALUE, TimeUnit.HOURS);
@@ -358,6 +372,7 @@ else if ( FloatType.class.isInstance( type ) )
 				return false;
 			}
 
+			IJ.showProgress( progress.getAndSet( 0 ), allBlocks.size() );
 			IOFunctions.println( new Date( System.currentTimeMillis() ) + ": Saved level s " + level + ", took: " + (System.currentTimeMillis() - time ) + " ms." );
 		}