mpicbg.spim.data.SpimDataException Java Examples

@Override
public boolean finish()
{
	XmlIoSpimData2 io = new XmlIoSpimData2( "" );

	try
	{
		io.save( spimData, new File( params.getXMLFile() ).getAbsolutePath() );
		
		IOFunctions.println( "(" + new Date( System.currentTimeMillis() ) + "): Saved xml '" + io.lastFileName() + "'." );

		// this spimdata object was not modified, we just wrote a new one
		return false;
	}
	catch ( SpimDataException e )
	{
		IOFunctions.println( "(" + new Date( System.currentTimeMillis() ) + "): Could not save xml '" + io.lastFileName() + "'." );
		e.printStackTrace();
		return false;
	}
}
 

@Override
public boolean finish()
{
	System.out.println( "finish()" );
	String path = params.getSeqFile().getAbsolutePath();
	try
	{
		new XmlIoSpimData2( "" ).save( spimData, path );

		IOFunctions.println( "(" + new Date( System.currentTimeMillis() ) + "): Saved xml '" + path + "'." );

		// this spimdata object was not modified, we just wrote a new one
		return false;
	}
	catch ( SpimDataException e )
	{
		IOFunctions.println( "(" + new Date( System.currentTimeMillis() ) + "): Could not save xml '" + path + "'." );
		e.printStackTrace();
		return false;
	}
}
 

public static < T extends AbstractSpimData< A >, A extends AbstractSequenceDescription< ?, ?, ? super ImgLoader > > void writeXML(
		final T spimData,
		final XmlIoAbstractSpimData< A, T > io,
		final Parameters params,
		final ProgressWriter progressWriter )
	throws SpimDataException
{
	final A seq = spimData.getSequenceDescription();
	final ArrayList< Partition > partitions = getPartitions( spimData, params );
	final Hdf5ImageLoader hdf5Loader = new Hdf5ImageLoader( params.hdf5File, partitions, null, false );
	seq.setImgLoader( hdf5Loader );
	spimData.setBasePath( params.seqFile.getParentFile() );
	try
	{
		if ( !params.onlyRunSingleJob || params.jobId == 0 )
			io.save( spimData, params.seqFile.getAbsolutePath() );
		progressWriter.setProgress( 1.0 );
	}
	catch ( final Exception e )
	{
		progressWriter.err().println( "Failed to write xml file " + params.seqFile );
		e.printStackTrace( progressWriter.err() );
	}
	progressWriter.out().println( "done" );
}
 

public BoundingBoxes fromXml( final Element allBoundingBoxes ) throws SpimDataException
{
	final BoundingBoxes boundingBoxes = super.fromXml( allBoundingBoxes );

	for ( final Element boundingBoxElement : allBoundingBoxes.getChildren( BOUNDINGBOX_TAG ) )
	{
		final String title = boundingBoxElement.getAttributeValue( BOUNDINGBOX_TAG_NAME );

		final int[] min = XmlHelpers.getIntArray( boundingBoxElement, BOUNDINGBOX_TAG_MIN );
		final int[] max = XmlHelpers.getIntArray( boundingBoxElement, BOUNDINGBOX_TAG_MAX );

		boundingBoxes.addBoundingBox( new BoundingBox( title, min, max ) );
	}

	return boundingBoxes;
}
 

public ViewInterestPoints fromXml( final Element allInterestPointLists, final File basePath, final Map< ViewId, ViewDescription > viewDescriptions ) throws SpimDataException
{
	final ViewInterestPoints viewsInterestPoints = super.fromXml( allInterestPointLists );
	viewsInterestPoints.createViewInterestPoints( viewDescriptions );

	for ( final Element viewInterestPointsElement : allInterestPointLists.getChildren( VIEWINTERESTPOINTSFILE_TAG ) )
	{
		final int timepointId = Integer.parseInt( viewInterestPointsElement.getAttributeValue( VIEWINTERESTPOINTS_TIMEPOINT_ATTRIBUTE_NAME ) );
		final int setupId = Integer.parseInt( viewInterestPointsElement.getAttributeValue( VIEWINTERESTPOINTS_SETUP_ATTRIBUTE_NAME ) );
		final String label = viewInterestPointsElement.getAttributeValue( VIEWINTERESTPOINTS_LABEL_ATTRIBUTE_NAME );
		final String parameters = viewInterestPointsElement.getAttributeValue( VIEWINTERESTPOINTS_PARAMETERS_ATTRIBUTE_NAME );

		final String interestPointFileName = viewInterestPointsElement.getTextTrim();

		final ViewId viewId = new ViewId( timepointId, setupId );
		final ViewInterestPointLists collection = viewsInterestPoints.getViewInterestPointLists( viewId );

		// we do not load the interestpoints nor the correspondinginterestpoints, we just do that once it is requested
		final InterestPointList list = new InterestPointList( basePath, new File( interestPointFileName ) );
		list.setParameters( parameters );
		collection.addInterestPointList( label, list );
	}

	return viewsInterestPoints;
}
 

public static void main( String[] args ) throws SpimDataException
{
	String xml = "/Users/spreibi/Documents/Grants and CV/BIMSB/Projects/CLARITY/Big Data Sticher/Dros_converted/dataset.xml";

	XmlIoSpimData2 io = new XmlIoSpimData2( null );
	final SpimData2 data = io.load( xml );
	System.out.println(  "chosen ds: " + Util.printCoordinates( askForDownsampling( data, false ) ) );
	System.exit( 0 );
}
 

@Override
public void saveXML()
{
	try
	{
		io.save( data, xml );

		for ( final SelectedViewDescriptionListener< AS > l : listeners )
			l.save();

		if ( SpimData2.class.isInstance( data ) )
		{
			final ViewInterestPoints vip = ( (SpimData2) data ).getViewInterestPoints();

			for ( final ViewInterestPointLists vipl : vip.getViewInterestPoints().values() )
			{
				for ( final String label : vipl.getHashMap().keySet() )
				{
					final InterestPointList ipl = vipl.getInterestPointList( label );
					ipl.saveInterestPoints( false );
					ipl.saveCorrespondingInterestPoints( false );
				}
			}
		}

		IOFunctions.println( "Saved XML '" + xml + "'." );
	}
	catch ( SpimDataException e )
	{
		IOFunctions.println( "Failed to save XML '" + xml + "': " + e );
		e.printStackTrace();
	}
}
 

@Override
public Element toXml( final SpimData2 spimData, final File xmlFileDirectory ) throws SpimDataException
{
	final Element root = super.toXml( spimData, xmlFileDirectory );

	root.addContent( xmlViewsInterestPoints.toXml( spimData.getViewInterestPoints() ) );
	root.addContent( xmlBoundingBoxes.toXml( spimData.getBoundingBoxes() ) );

	return root;
}
 

@Override
public SpimData2 fromXml( final Element root, final File xmlFile ) throws SpimDataException
{
	final SpimData2 spimData = super.fromXml( root, xmlFile );
	final SequenceDescription seq = spimData.getSequenceDescription();

	final ViewInterestPoints viewsInterestPoints;
	Element elem = root.getChild( xmlViewsInterestPoints.getTag() );
	if ( elem == null )
	{
		viewsInterestPoints = new ViewInterestPoints();
		viewsInterestPoints.createViewInterestPoints( seq.getViewDescriptions() );
	}
	else
	{
		viewsInterestPoints = xmlViewsInterestPoints.fromXml( elem, spimData.getBasePath(), seq.getViewDescriptions() );
	}
	spimData.setViewsInterestPoints( viewsInterestPoints );

	final BoundingBoxes boundingBoxes;
	elem = root.getChild( xmlBoundingBoxes.getTag() );
	if ( elem == null )
		boundingBoxes = new BoundingBoxes();
	else
		boundingBoxes = xmlBoundingBoxes.fromXml( elem );
	spimData.setBoundingBoxes( boundingBoxes );

	return spimData;
}
 

public static void run(File xmlFile) {
	BDVRenderer renderer;
	try {
		renderer = new BDVRenderer(xmlFile);
		AnimationEditor editor = new AnimationEditor(renderer, Default3DRecordingProvider.getInstance());
		editor.setVisible(true);
	} catch (SpimDataException e) {
		e.printStackTrace();
		IJ.handleException(e);
	}
}
 

public void saveXML()
{
	try
	{
		io.save( data, xml );

		for ( final SelectedViewDescriptionListener< AS > l : listeners )
			l.save();

		if ( SpimData2.class.isInstance( data ) )
		{
			final ViewInterestPoints vip = ( (SpimData2)data ).getViewInterestPoints();
			
			for ( final ViewInterestPointLists vipl : vip.getViewInterestPoints().values() )
			{
				for ( final String label : vipl.getHashMap().keySet() )
				{
					final InterestPointList ipl = vipl.getInterestPointList( label );

					if ( ipl.getInterestPoints() == null )
						ipl.loadInterestPoints();
					
					ipl.saveInterestPoints();

					if ( ipl.getCorrespondingInterestPoints() == null )
						ipl.loadCorrespondingInterestPoints();

					ipl.saveCorrespondingInterestPoints();
				}
			}
		}

		IOFunctions.println( "Saved XML '" + xml + "'." );
	}
	catch ( SpimDataException e )
	{
		IOFunctions.println( "Failed to save XML '" + xml + "': " + e );
		e.printStackTrace();
	}
}
 

protected AS parseXML( final String xmlFilename ) throws SpimDataException
{
	return io.load( xmlFilename );
}
 

@Override
public void save( final SpimData2 spimData, String xmlFilename ) throws SpimDataException
{
	if ( clusterExt != null && clusterExt.length() > 0 )
	{
		if ( xmlFilename.toLowerCase().endsWith( ".xml" ) )
		{
			xmlFilename =
					xmlFilename.substring( 0, xmlFilename.length() - 4 ) + "." + this.clusterExt +
					xmlFilename.substring( xmlFilename.length() - 4, xmlFilename.length() );
		}
		else
		{
			xmlFilename += this.clusterExt + ".xml";
		}
	}

	this.lastFileName = xmlFilename;

	// fist make a copy of the XML and save it to not loose it
	if ( new File( xmlFilename ).exists() )
	{
		int maxExistingBackup = 0;
		for ( int i = 1; i < numBackups; ++i )
			if ( new File( xmlFilename + "~" + i ).exists() )
				maxExistingBackup = i;
			else
				break;

		// copy the backups
		try
		{
			for ( int i = maxExistingBackup; i >= 1; --i )
				copyFile( new File( xmlFilename + "~" + i ), new File( xmlFilename + "~" + (i + 1) ) );

			copyFile( new File( xmlFilename ), new File( xmlFilename + "~1" ) );
		}
		catch ( final IOException e )
		{
			IOFunctions.println( "Could not save backup of XML file: " + e );
			e.printStackTrace();
		}
	}

	super.save( spimData, xmlFilename );
}
 

@Override
public void run( final String arg0 )
{
	final LoadParseQueryXML lpq = new LoadParseQueryXML();

	if ( !lpq.queryXML( "Resaving as TIFF", "Resave", true, true, true, true ) )
		return;

	final ProgressWriter progressWriter = new ProgressWriterIJ();
	progressWriter.out().println( "starting export..." );
	
	final Parameters params = getParameters();
	
	if ( params == null )
		return;

	final SpimData2 data = lpq.getData();
	final List< ViewId > viewIds = SpimData2.getAllViewIdsSorted( data, lpq.getViewSetupsToProcess(), lpq.getTimePointsToProcess() );

	// write the TIFF's
	writeTIFF( data, viewIds, new File( params.xmlFile ).getParent(), params.compress, progressWriter );

	// write the XML
	try
	{
		final Pair< SpimData2, List< String > > result = createXMLObject( data, viewIds, params );
		progressWriter.setProgress( 0.95 );

		// write the XML
		lpq.getIO().save( result.getA(), new File( params.xmlFile ).getAbsolutePath() );

		// copy the interest points if they exist
		copyInterestPoints( data.getBasePath(), new File( params.xmlFile ).getParentFile(), result.getB() );
	}
	catch ( SpimDataException e )
	{
		IOFunctions.println( "(" + new Date( System.currentTimeMillis() ) + "): Could not save xml '" + params.xmlFile + "'." );
		e.printStackTrace();
	}
	finally
	{
		progressWriter.setProgress( 1.00 );
		IOFunctions.println( "(" + new Date( System.currentTimeMillis() ) + "): Saved xml '" + params.xmlFile + "'." );
	}
}
 

@Override
public void run( final String arg0 )
{
	boolean rememberClusterProcessing = Toggle_Cluster_Options.displayClusterProcessing;
	Toggle_Cluster_Options.displayClusterProcessing = false;

	final LoadParseQueryXML xml = new LoadParseQueryXML();

	if ( !xml.queryXML( "Resaving as HDF5", "Resave", true, true, true, true ) )
		return;

	Toggle_Cluster_Options.displayClusterProcessing = rememberClusterProcessing;

	// load all dimensions if they are not known (required for estimating the mipmap layout)
	if ( loadDimensions( xml.getData(), xml.getViewSetupsToProcess() ) )
	{
		// save the XML again with the dimensions loaded
		SpimData2.saveXML( xml.getData(), xml.getXMLFileName(), xml.getClusterExtension() );
	}

	final Map< Integer, ExportMipmapInfo > perSetupExportMipmapInfo = proposeMipmaps( xml.getViewSetupsToProcess() );

	Generic_Resave_HDF5.lastExportPath = LoadParseQueryXML.defaultXMLfilename;

	final int firstviewSetupId = xml.getData().getSequenceDescription().getViewSetupsOrdered().get( 0 ).getId();
	final Parameters params = Generic_Resave_HDF5.getParameters( perSetupExportMipmapInfo.get( firstviewSetupId ), true, true );

	if ( params == null )
		return;

	LoadParseQueryXML.defaultXMLfilename = params.getSeqFile().toString();

	final ProgressWriter progressWriter = new ProgressWriterIJ();
	progressWriter.out().println( "starting export..." );

	final SpimData2 data = xml.getData();
	final List< ViewId > viewIds = SpimData2.getAllViewIdsSorted( data, xml.getViewSetupsToProcess(), xml.getTimePointsToProcess() );

	// write hdf5
	Generic_Resave_HDF5.writeHDF5( reduceSpimData2( data, viewIds ), params, progressWriter );

	// write xml sequence description
	if ( !params.onlyRunSingleJob || params.jobId == 0 )
	{
		try
		{
			final Pair< SpimData2, List< String > > result = createXMLObject( data, viewIds, params, progressWriter, false );

			xml.getIO().save( result.getA(), params.seqFile.getAbsolutePath() );
			progressWriter.setProgress( 0.95 );
			
			// copy the interest points if they exist
			Resave_TIFF.copyInterestPoints( xml.getData().getBasePath(), params.getSeqFile().getParentFile(), result.getB() );
		}
		catch ( SpimDataException e )
		{
			IOFunctions.println( "(" + new Date( System.currentTimeMillis() ) + "): Could not save xml '" + params.getSeqFile() + "': " + e );
			throw new RuntimeException( e );
		}
		finally
		{
			IOFunctions.println( "(" + new Date( System.currentTimeMillis() ) + "): Saved xml '" + params.getSeqFile() + "'." );
		}
	}
	progressWriter.setProgress( 1.0 );
	progressWriter.out().println( "done" );
}
 

public void openBDV(File xmlFile) throws SpimDataException {
	options = ViewerOptions.options();
	viewer = BigDataViewer.open(xmlFile.getAbsolutePath(), xmlFile.getName(), new ProgressWriterIJ(), options);
}
 

public BDVRenderer(File xmlFile) throws SpimDataException {
		openBDV(xmlFile);
//		this.tgtW = 0; // TODO
//		this.tgtH = 0; // TODO

		float[] pdOut = new float[] {1, 1, 1};
		float[] pdIn  = new float[] {1, 1, 1};

		this.rotationCenter = calculateRotationCenter();
		System.out.println("rotcenter: " + Arrays.toString(rotationCenter));
		float[] rotcenter = rotationCenter.clone();

		CombinedTransform transformation = new CombinedTransform(pdIn, pdOut, rotcenter);
		DisplayMode mode = viewer.getViewer().getVisibilityAndGrouping().getDisplayMode();
		int tp = viewer.getViewer().getState().getCurrentTimepoint();
		Interpolation interpolation = viewer.getViewer().getState().getInterpolation();
		int currentSource = viewer.getViewer().getState().getCurrentSource();
		int nSources = viewer.getViewer().getState().numSources();
		double[] min = new double[nSources];
		double[] max = new double[nSources];
		Color[] colors = new Color[nSources];

		SetupAssignments setupAssignments = viewer.getSetupAssignments();
		for(int s = 0; s < nSources; s++) {
			final ConverterSetup setup = setupAssignments.getConverterSetups().get(s);
			colors[s] = new Color(setup.getColor().get());
			min[s] = setup.getDisplayRangeMin();
			max[s] = setup.getDisplayRangeMax();
		}

		this.rs = new BDVRenderingState(0,
				mode,
				tp,
				interpolation,
				currentSource, // current source
				transformation,
				colors,
				min,
				max);

	}