Merge remote-tracking branch 'github/towards-spimdata' into bounding-box

fiji/src/main/java/bdv/ij/ResavePlugin.java

-package bdv.ij;
-
-import fiji.util.gui.GenericDialogPlus;
-import ij.IJ;
-import ij.gui.DialogListener;
-import ij.gui.GenericDialog;
-import ij.plugin.PlugIn;
-
-import java.awt.AWTEvent;
-import java.awt.Checkbox;
-import java.awt.TextField;
-import java.awt.event.ItemEvent;
-import java.io.File;
-import java.util.Map;
-
-import javax.swing.JFileChooser;
-import javax.swing.filechooser.FileFilter;
-
-import mpicbg.spim.data.SpimDataException;
-import mpicbg.spim.data.generic.AbstractSpimData;
-import mpicbg.spim.data.generic.XmlIoAbstractSpimData;
-import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription;
-import mpicbg.spim.data.sequence.ImgLoader;
-import bdv.export.ExportMipmapInfo;
-import bdv.export.ProgressWriter;
-import bdv.export.ProposeMipmaps;
-import bdv.export.SubTaskProgressWriter;
-import bdv.export.WriteSequenceToHdf5;
-import bdv.ij.util.PluginHelper;
-import bdv.ij.util.ProgressWriterIJ;
-import bdv.img.hdf5.Hdf5ImageLoader;
-import bdv.spimdata.SpimDataMinimal;
-import bdv.spimdata.XmlIoSpimDataMinimal;
-
-public class ResavePlugin implements PlugIn
-{
-	public static void main( final String[] args )
-	{
-		new ResavePlugin().run( null );
-	}
-
-	public static class Parameters
-	{
-		boolean setMipmapManual;
-		int[][] resolutions;
-		int[][] subdivisions;
-		File seqFile;
-		File hdf5File;
-
-		public Parameters( final boolean setMipmapManual, final int[][] resolutions, final int[][] subdivisions, final File seqFile, final File hdf5File )
-		{
-			this.setMipmapManual = setMipmapManual;
-			this.resolutions = resolutions;
-			this.subdivisions = subdivisions;
-			this.seqFile = seqFile;
-			this.hdf5File = hdf5File;
-		}
-		
-		public void setSeqFile( final File seqFile ) { this.seqFile = seqFile; }
-		public void setHDF5File( final File hdf5File ) { this.hdf5File = hdf5File; }
-		public void setResolutions( final int[][] resolutions ) { this.resolutions = resolutions; }
-		public void setSubdivisions( final int[][] subdivisions ) { this.subdivisions = subdivisions; }
-		public void setMipmapManual( final boolean setMipmapManual ) { this.setMipmapManual = setMipmapManual; }
-		
-		public File getSeqFile() { return seqFile; }
-		public File getHDF5File() { return hdf5File; }
-		public int[][] getResolutions() { return resolutions; }
-		public int[][] getSubdivisions() { return subdivisions; }
-		public boolean getMipmapManual() { return setMipmapManual; }
-	}
-
-	@Override
-	public void run( final String arg )
-	{
-		final File file = getInputXML();
-		if ( file == null )
-			return;
-		
-		final XmlIoSpimDataMinimal io = new XmlIoSpimDataMinimal();
-		SpimDataMinimal spimData;
-		try
-		{
-			spimData = io.load( file.getAbsolutePath() );
-		}
-		catch ( final SpimDataException e )
-		{
-			throw new RuntimeException( e );
-		}
-
-		final Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo = ProposeMipmaps.proposeMipmaps( spimData.getSequenceDescription() );
-
-		final Parameters params = getParameters( perSetupExportMipmapInfo.get( 0 ), true );
-		if ( params == null )
-			return;
-
-		final ProgressWriter progressWriter = new ProgressWriterIJ();
-		progressWriter.out().println( "starting export..." );
-
-		// write hdf5
-		writeHDF5( spimData.getSequenceDescription(), params, perSetupExportMipmapInfo, progressWriter );
-		
-		// write xml sequence description
-		writeXML( spimData, io, params.seqFile, params.hdf5File, progressWriter );
-	}
-	
-	public static void writeHDF5( final AbstractSequenceDescription< ?, ?, ? > seq, final Parameters params, final Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo, final ProgressWriter progressWriter )
-	{
-		final boolean setMipmapManual = params.setMipmapManual;
-		final int[][] manualResolutions = params.resolutions;
-		final int[][] manualSubdivisions = params.subdivisions;
-
-		if ( setMipmapManual )
-			WriteSequenceToHdf5.writeHdf5File( seq, manualResolutions, manualSubdivisions, params.hdf5File, new SubTaskProgressWriter( progressWriter, 0, 0.95 ) );
-		else
-			WriteSequenceToHdf5.writeHdf5File( seq, perSetupExportMipmapInfo, params.hdf5File, new SubTaskProgressWriter( progressWriter, 0, 0.95 ) );
-	}
-	
-	public static < T extends AbstractSpimData< A >, A extends AbstractSequenceDescription< ?, ?, ? super ImgLoader< ? > > > void writeXML(
-			final T spimData,
-			final XmlIoAbstractSpimData< A, T > io,
-			final File seqFile,
-			final File hdf5File,
-			final ProgressWriter progressWriter )
-	{
-		final A seq = spimData.getSequenceDescription();
-		final Hdf5ImageLoader hdf5Loader = new Hdf5ImageLoader( hdf5File, null, null, false );
-		seq.setImgLoader( hdf5Loader );
-		spimData.setBasePath( seqFile.getParentFile() );
-
-		try
-		{
-			io.save( spimData, seqFile.getAbsolutePath() );
-		}
-		catch ( final SpimDataException e )
-		{
-			throw new RuntimeException( e );
-		}
-		
-		progressWriter.setProgress( 1.0 );
-		progressWriter.out().println( "done" );
-	}
-
-	static boolean lastSetMipmapManual = false;
-
-	static String lastSubsampling = "{1,1,1}, {2,2,1}, {4,4,2}";
-
-	static String lastChunkSizes = "{16,16,16}, {16,16,16}, {16,16,16}";
-
-	public static String lastExportPath = "/Users/pietzsch/Desktop/spimrec2.xml";
-
-	public static File getInputXML()
-	{
-		final JFileChooser fileChooser = new JFileChooser();
-		fileChooser.setFileFilter( new FileFilter()
-		{
-			@Override
-			public String getDescription()
-			{
-				return "xml files";
-			}
-
-			@Override
-			public boolean accept( final File f )
-			{
-				if ( f.isDirectory() )
-					return true;
-				if ( f.isFile() )
-				{
-					final String s = f.getName();
-					final int i = s.lastIndexOf('.');
-					if (i > 0 &&  i < s.length() - 1) {
-						final String ext = s.substring(i+1).toLowerCase();
-						return ext.equals( "xml" );
-					}
-				}
-				return false;
-			}
-		} );
-
-		if ( fileChooser.showOpenDialog( null ) == JFileChooser.APPROVE_OPTION )
-			return fileChooser.getSelectedFile();
-		else
-			return null;
-	}
-	
-	public static Parameters getParameters( final ExportMipmapInfo autoMipmapSettings, final boolean askForXMLPath )
-	{
-		while ( true )
-		{
-			final GenericDialogPlus gd = new GenericDialogPlus( "Export for BigDataViewer" );
-
-			gd.addCheckbox( "manual mipmap setup", lastSetMipmapManual );
-			final Checkbox cManualMipmap = ( Checkbox ) gd.getCheckboxes().lastElement();
-			gd.addStringField( "Subsampling factors", lastSubsampling, 25 );
-			final TextField tfSubsampling = ( TextField ) gd.getStringFields().lastElement();
-			gd.addStringField( "Hdf5 chunk sizes", lastChunkSizes, 25 );
-			final TextField tfChunkSizes = ( TextField ) gd.getStringFields().lastElement();
-
-			if ( askForXMLPath )
-				PluginHelper.addSaveAsFileField( gd, "Export path", lastExportPath, 25 );
-
-			final String autoSubsampling = ProposeMipmaps.getArrayString( autoMipmapSettings.getExportResolutions() );
-			final String autoChunkSizes = ProposeMipmaps.getArrayString( autoMipmapSettings.getSubdivisions() );
-			gd.addDialogListener( new DialogListener()
-			{
-				@Override
-				public boolean dialogItemChanged( final GenericDialog dialog, final AWTEvent e )
-				{
-					if ( e instanceof ItemEvent && e.getID() == ItemEvent.ITEM_STATE_CHANGED && e.getSource() == cManualMipmap )
-					{
-						final boolean useManual = cManualMipmap.getState();
-						tfSubsampling.setEnabled( useManual );
-						tfChunkSizes.setEnabled( useManual );
-						if ( !useManual )
-						{
-							tfSubsampling.setText( autoSubsampling );
-							tfChunkSizes.setText( autoChunkSizes );
-						}
-					}
-					return true;
-				}
-			} );
-
-			tfSubsampling.setEnabled( lastSetMipmapManual );
-			tfChunkSizes.setEnabled( lastSetMipmapManual );
-			if ( !lastSetMipmapManual )
-			{
-				tfSubsampling.setText( autoSubsampling );
-				tfChunkSizes.setText( autoChunkSizes );
-			}
-
-			gd.showDialog();
-			if ( gd.wasCanceled() )
-				return null;
-
-			lastSetMipmapManual = gd.getNextBoolean();
-			lastSubsampling = gd.getNextString();
-			lastChunkSizes = gd.getNextString();
-			lastExportPath = gd.getNextString();
-
-			// parse mipmap resolutions and cell sizes
-			final int[][] resolutions = PluginHelper.parseResolutionsString( lastSubsampling );
-			final int[][] subdivisions = PluginHelper.parseResolutionsString( lastChunkSizes );
-			if ( resolutions.length == 0 )
-			{
-				IJ.showMessage( "Cannot parse subsampling factors " + lastSubsampling );
-				continue;
-			}
-			if ( subdivisions.length == 0 )
-			{
-				IJ.showMessage( "Cannot parse hdf5 chunk sizes " + lastChunkSizes );
-				continue;
-			}
-			else if ( resolutions.length != subdivisions.length )
-			{
-				IJ.showMessage( "subsampling factors and hdf5 chunk sizes must have the same number of elements" );
-				continue;
-			}
-
-			final File seqFile, hdf5File;
-
-			if ( askForXMLPath )
-			{
-				String seqFilename = lastExportPath;
-				if ( !seqFilename.endsWith( ".xml" ) )
-					seqFilename += ".xml";
-				seqFile = new File( seqFilename );
-				final File parent = seqFile.getParentFile();
-				if ( parent == null || !parent.exists() || !parent.isDirectory() )
-				{
-					IJ.showMessage( "Invalid export filename " + seqFilename );
-					continue;
-				}
-				final String hdf5Filename = seqFilename.substring( 0, seqFilename.length() - 4 ) + ".h5";
-				hdf5File = new File( hdf5Filename );
-			}
-			else
-			{
-				seqFile = hdf5File = null;
-			}
-
-			return new Parameters( lastSetMipmapManual, resolutions, subdivisions, seqFile, hdf5File );
-		}
-	}
-}