net.imglib2.img.cell.CellImgFactory Java Examples

@Test
public void testImageFactory() {
	final Dimensions dim = new FinalDimensions(10, 10, 10);

	@SuppressWarnings("unchecked")
	final Img<DoubleType> arrayImg = (Img<DoubleType>) ops.run(
		CreateImgFromDimsAndType.class, dim, new DoubleType(),
		new ArrayImgFactory<DoubleType>());
	final Class<?> arrayFactoryClass = arrayImg.factory().getClass();
	assertEquals("Image Factory: ", ArrayImgFactory.class, arrayFactoryClass);

	@SuppressWarnings("unchecked")
	final Img<DoubleType> cellImg = (Img<DoubleType>) ops.run(
		CreateImgFromDimsAndType.class, dim, new DoubleType(),
		new CellImgFactory<DoubleType>());
	final Class<?> cellFactoryClass = cellImg.factory().getClass();
	assertEquals("Image Factory: ", CellImgFactory.class, cellFactoryClass);
}
 

@SuppressWarnings("unchecked")
@Test
public void testImageFactory() {

	final Dimensions dim = new FinalDimensions( 10, 10, 10 );

	assertEquals("Labeling Factory: ", ArrayImgFactory.class,
		((Img<?>) ((ImgLabeling<String, ?>) ops.run(
			DefaultCreateImgLabeling.class, dim, null,
			new ArrayImgFactory<IntType>())).getIndexImg()).factory().getClass());

	assertEquals("Labeling Factory: ", CellImgFactory.class,
		((Img<?>) ((ImgLabeling<String, ?>) ops.run(
			DefaultCreateImgLabeling.class, dim, null,
			new CellImgFactory<IntType>())).getIndexImg()).factory().getClass());

}
 

protected ImgFactory<? extends NativeType<?>> selectImgFactory(final SlideBook6MetaData meta) {
    int[] dims = meta.imageSize(0);
    long maxNumPixels = dims[0];
    maxNumPixels *= dims[1];
    maxNumPixels *= dims[2];

    String s = "Maximum number of pixels in any view: n=" + Long.toString(maxNumPixels) +
            " px ";

    if (maxNumPixels < Integer.MAX_VALUE) {
        IOFunctions.println(s + "< " + Integer.MAX_VALUE + ", using ArrayImg.");
        return new ArrayImgFactory<FloatType>();
    } else {
        IOFunctions.println(s + ">= " + Integer.MAX_VALUE + ", using CellImg.");
        return new CellImgFactory<FloatType>(256);
    }
}
 

protected < T extends NativeType< T > > Img< T > instantiateImg( final long[] dim, final T type )
{
	Img< T > img;
	
	try
	{
		img = getImgFactory().imgFactory( type ).create( dim, type );
	}
	catch ( Exception e1 )
	{
		try
		{
			img = new CellImgFactory< T >( 256 ).create( dim, type );
		}
		catch ( Exception e2 )
		{
			img = null;
		}
	}
	
	return img;
}
 

private CellGrid createCellGrid(final long[] dimensions,
	final Fraction entitiesPerPixel)
{
	CellImgFactory.verifyDimensions(dimensions);
	final int n = dimensions.length;

	final int[] defaultDims = new int[dimensions.length];
	for (int d = 0; d < defaultDims.length; d++) {
		defaultDims[d] = dimensions[d] < defaultCellDimensions[d] ? //
			(int) dimensions[d] : defaultCellDimensions[d];
	}

	final int[] cellDimensions = CellImgFactory.getCellDimensions(defaultDims,
		n, entitiesPerPixel);
	return new CellGrid(dimensions, cellDimensions);
}
 

public CellImg<ByteType, ?> generateByteTestCellImg(final boolean fill,
	final long... dims)
{
	final CellImg<ByteType, ?> img = new CellImgFactory<ByteType>().create(dims,
		new ByteType());

	if (fill) {
		final Cursor<ByteType> c = img.cursor();
		while (c.hasNext())
			c.next().set((byte) pseudoRandom());
	}

	return img;
}
 

public CellImg<ByteType, ?> generateByteTestCellImg(final boolean fill,
	final int[] cellDims, final long... dims)
{
	final CellImg<ByteType, ?> img = new CellImgFactory<ByteType>(cellDims)
		.create(dims, new ByteType());

	if (fill) {
		final Cursor<ByteType> c = img.cursor();
		while (c.hasNext())
			c.next().set((byte) pseudoRandom());
	}

	return img;
}
 

public static Parameters getParameters()
{
	final GenericDialogPlus gd = new GenericDialogPlus( "Resave dataset as TIFF" );

	if ( defaultPath == null )
		defaultPath = LoadParseQueryXML.defaultXMLfilename;

	PluginHelper.addSaveAsFileField( gd, "Select new XML", defaultPath, 80 );
	
	gd.addChoice( "ImgLib2_data_container", StackList.imglib2Container, StackList.imglib2Container[ defaultContainer ] );
	gd.addCheckbox( "Lossless compression of TIFF files (ZIP)", defaultCompress );
	gd.addMessage( "Use ArrayImg if -ALL- input views are smaller than ~2048x2048x500 px (2^31 px), or if the\n" +
				   "program throws an OutOfMemory exception while processing.  CellImg is slower, but more\n" +
			       "memory efficient and supports much larger file sizes only limited by the RAM of the machine.", 
			       new Font( Font.SANS_SERIF, Font.ITALIC, 11 ) );

	gd.showDialog();
	
	if ( gd.wasCanceled() )
		return null;

	final Parameters params = new Parameters();
	
	params.xmlFile = gd.getNextString();
	
	if ( !params.xmlFile.endsWith( ".xml" ) )
		params.xmlFile += ".xml";

	params.compress = defaultCompress = gd.getNextBoolean();

	defaultPath = LoadParseQueryXML.defaultXMLfilename = params.xmlFile;

	if ( ( defaultContainer = gd.getNextChoiceIndex() ) == 0 )
		params.imgFactory = new ArrayImgFactory< FloatType >();
	else
		params.imgFactory = new CellImgFactory< FloatType >();

	return params;
}
 

protected ImgFactory< ? extends NativeType< ? > > selectImgFactory( final LightSheetZ1MetaData meta )
{
	long maxNumPixels = 0;

	for ( int a = 0; a < meta.numAngles(); ++a )
	{
		final int[] dim = meta.imageSizes().get( a );

		long n = 1;

		for ( int d = 0; d < dim.length; ++d )
		{
			n *= (long)dim[ d ];

			if ( dim[ d ] <= 0 )
			{
				IOFunctions.println( "Dimensions couldn't be read from metadata, using CellImg(256)." );
				return new CellImgFactory< FloatType >( 256 );
			}
		}

		maxNumPixels = Math.max( n, maxNumPixels );
	}

	int smallerLog2 = (int)Math.ceil( Math.log( maxNumPixels ) / Math.log( 2 ) );

	String s = "Maximum number of pixels in any view: n=" + maxNumPixels + 
			" (2^" + (smallerLog2-1) + " < n < 2^" + smallerLog2 + " px), ";

	if ( smallerLog2 <= 31 )
	{
		IOFunctions.println( s + "using ArrayImg." );
		return new ArrayImgFactory< FloatType >();
	}
	else
	{
		IOFunctions.println( s + "using CellImg(256)." );
		return new CellImgFactory< FloatType >( 256 );
	}
}
 

public < T extends ComplexType< T > & NativeType < T > > ImgFactory< T > getImgFactory( final T type )
{
	final ImgFactory< T > imgFactory;
	
	if ( this.getImgType() == 0 )
		imgFactory = new ArrayImgFactory< T >();
	else if ( this.getImgType() == 1 )
		imgFactory = new ImagePlusImgFactory< T >();
	else
		imgFactory = new CellImgFactory<T>( 256 );

	return imgFactory;
}
 

@Override
public ImgFactory<T> calculate() {
	return (dims == null || Intervals.numElements(dims) <= Integer.MAX_VALUE)
		? new ArrayImgFactory<>() : new CellImgFactory<>();
}
 

@Override
public SlideBook6ImgLoader fromXml(
		final Element elem, File basePath,
		final AbstractSequenceDescription<?, ?, ?> sequenceDescription )
{
	try
	{
		final File path = loadPath( elem, DIRECTORY_TAG, basePath );
		final String masterFile = XmlHelpers.getText( elem, MASTER_FILE_TAG );
		final String container = XmlHelpers.getText( elem, IMGLIB2CONTAINER_PATTERN_TAG );

		final ImgFactory< FloatType > imgFactory;

		if ( container == null )
		{
			System.out.println( "WARNING: No Img implementation defined in XML, using ArrayImg." );

			// if no factory is defined we define an ArrayImgFactory
			imgFactory = new ArrayImgFactory< FloatType >();
		}
		else
		{
			if ( container.toLowerCase().contains( "cellimg" ) )
			{
				imgFactory = new CellImgFactory< FloatType >( 256 );
			}
			else if ( container.toLowerCase().contains( "arrayimg" ) )
			{
				imgFactory = new ArrayImgFactory< FloatType >();
			}
			else if ( container.toLowerCase().contains( "planarimg" ) )
			{
				imgFactory = new PlanarImgFactory< FloatType >();
			}
			else
			{
			// if factory is unknown we define an ArrayImgFactory
			imgFactory = new ArrayImgFactory< FloatType >();
				
				System.out.println( "WARNING: Unknown Img implementation defined in XML:'" + container + "', using ArrayImg." );
			}
		}

		return new SlideBook6ImgLoader( new File( path, masterFile ), imgFactory, sequenceDescription );
	}
	catch ( final Exception e )
	{
		throw new RuntimeException( e );
	}
}
 

@Override
public LightSheetZ1ImgLoader fromXml(
		final Element elem, File basePath,
		final AbstractSequenceDescription<?, ?, ?> sequenceDescription )
{
	try
	{
		final File path = loadPath( elem, DIRECTORY_TAG, basePath );
		final String masterFile = XmlHelpers.getText( elem, MASTER_FILE_TAG );
		final String container = XmlHelpers.getText( elem, IMGLIB2CONTAINER_PATTERN_TAG );

		final ImgFactory< FloatType > imgFactory;

		if ( container == null )
		{
			System.out.println( "WARNING: No Img implementation defined in XML, using ArrayImg." );

			// if no factory is defined we define an ArrayImgFactory
			imgFactory = new ArrayImgFactory< FloatType >();
		}
		else
		{
			if ( container.toLowerCase().contains( "cellimg" ) )
			{
				imgFactory = new CellImgFactory< FloatType >( 256 );
			}
			else if ( container.toLowerCase().contains( "arrayimg" ) )
			{
				imgFactory = new ArrayImgFactory< FloatType >();
			}
			else if ( container.toLowerCase().contains( "planarimg" ) )
			{
				imgFactory = new PlanarImgFactory< FloatType >();
			}
			else
			{
				// if factory is unknown we define an ArrayImgFactory
				imgFactory = new ArrayImgFactory< FloatType >();
				
				System.out.println( "WARNING: Unknown Img implementation defined in XML:'" + container + "', using ArrayImg." );
			}
		}

		return new LightSheetZ1ImgLoader( new File( path, masterFile ), imgFactory, sequenceDescription );
	}
	catch ( final Exception e )
	{
		throw new RuntimeException( e );
	}
}
 

@Override
public T fromXml( final Element elem, final File basePath, final AbstractSequenceDescription< ?, ?, ? > sequenceDescription )
{
	try
	{
		File path = loadPath( elem, DIRECTORY_TAG, basePath );
		String fileNamePattern = XmlHelpers.getText( elem, FILE_PATTERN_TAG );

		int layoutTP = XmlHelpers.getInt( elem, LAYOUT_TP_TAG );
		int layoutChannels = XmlHelpers.getInt( elem, LAYOUT_CHANNEL_TAG );
		int layoutIllum = XmlHelpers.getInt( elem, LAYOUT_ILLUMINATION_TAG );
		int layoutAngles = XmlHelpers.getInt( elem, LAYOUT_ANGLE_TAG );

		final String container = XmlHelpers.getText( elem, IMGLIB2CONTAINER_PATTERN_TAG );
		ImgFactory< FloatType > imgFactory;
		if ( container == null )
		{
			System.out.println( "WARNING: No Img implementation defined, using ArrayImg." );

			// if no factory is defined we define an ArrayImgFactory
			imgFactory = new ArrayImgFactory< FloatType >();
		}
		else
		{
			if ( container.toLowerCase().contains( "cellimg" ) )
			{
				imgFactory = new CellImgFactory< FloatType >( 256 );
			}
			else if ( container.toLowerCase().contains( "arrayimg" ) )
			{
				imgFactory = new ArrayImgFactory< FloatType >();
			}
			else if ( container.toLowerCase().contains( "planarimg" ) )
			{
				imgFactory = new PlanarImgFactory< FloatType >();
			}
			else
			{
				// if factory is unknown we define an ArrayImgFactory
				imgFactory = new ArrayImgFactory< FloatType >();
				
				System.out.println( "WARNING: Unknown Img implementation '" + container + "', using ArrayImg." );
			}
		}
		
		return createImgLoader( path, fileNamePattern, imgFactory, layoutTP, layoutChannels, layoutIllum, layoutAngles, sequenceDescription );
	}
	catch ( final Exception e )
	{
		throw new RuntimeException( e );
	}
}
 

@Override
public boolean parseAdditionalParameters( final GenericDialog gd )
{
	defaultFFTImgType = gd.getNextChoiceIndex();

	if ( defaultFFTImgType == 0 )
		computeFactory = new ArrayImgFactory< FloatType >();
	else if ( defaultFFTImgType == 1 )
		computeFactory = new ImagePlusImgFactory< FloatType >();
	else
		computeFactory = new CellImgFactory< FloatType >( 256 );

	saveMemory = defaultSaveMemory = gd.getNextBoolean();
	defaultIterationType = gd.getNextChoiceIndex();

	if ( defaultIterationType == 0 )
		iterationType = PSFTYPE.OPTIMIZATION_II;
	else if ( defaultIterationType == 1 )
		iterationType = PSFTYPE.OPTIMIZATION_I;
	else if ( defaultIterationType == 2 )
		iterationType = PSFTYPE.EFFICIENT_BAYESIAN;
	else //if ( defaultIterationType == 3 )
		iterationType = PSFTYPE.INDEPENDENT;

	defaultWeightType = gd.getNextChoiceIndex();

	if ( defaultWeightType == 0 )
		weightType = WeightType.PRECOMPUTED_WEIGHTS;
	else if ( defaultWeightType == 1 )
		weightType = WeightType.VIRTUAL_WEIGHTS;
	else if ( defaultWeightType == 2 )
		weightType = WeightType.NO_WEIGHTS;
	else
		weightType = WeightType.WEIGHTS_ONLY;

	osemspeedupIndex = defaultOSEMspeedupIndex = gd.getNextChoiceIndex();
	numIterations = defaultNumIterations = (int)Math.round( gd.getNextNumber() );
	debugMode = defaultDebugMode = gd.getNextBoolean();
	adjustBlending = defaultAdjustBlending = gd.getNextBoolean();
	useTikhonovRegularization = defaultUseTikhonovRegularization = gd.getNextBoolean();
	lambda = defaultLambda = gd.getNextNumber();
	blockSizeIndex = defaultBlockSizeIndex = gd.getNextChoiceIndex();
	computationTypeIndex = defaultComputationTypeIndex = gd.getNextChoiceIndex();
	extractPSFIndex = defaultExtractPSF = gd.getNextChoiceIndex();
	displayPSF = defaultDisplayPSF = gd.getNextChoiceIndex();

	return true;
}