Java IOFunctions.printlnSafe方法代碼示例

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
@Override
public RandomAccessibleInterval< UnsignedShortType > getImage( final ViewId view )
{
	try
	{
		final MultipageTiffReader r = new MultipageTiffReader( mmFile );

		final ArrayImg< UnsignedShortType, ? > img = ArrayImgs.unsignedShorts( r.width(), r.height(), r.depth() );
		final BasicViewDescription< ? > vd = sequenceDescription.getViewDescriptions().get( view );

		populateImage( img, vd, r );

		updateMetaDataCache( view, r.width(), r.height(), r.depth(), r.calX(), r.calY(), r.calZ() );

		r.close();

		return img;
	}
	catch ( Exception e )
	{
		IOFunctions.printlnSafe( "Failed to load viewsetup=" + view.getViewSetupId() + " timepoint=" + view.getTimePointId() + ": " + e );
		e.printStackTrace();
		return null;
	}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
@Override
protected void loadMetaData( final ViewId view )
{
	try
	{
		final MultipageTiffReader r = new MultipageTiffReader( mmFile );

		updateMetaDataCache( view, r.width(), r.height(), r.depth(), r.calX(), r.calY(), r.calZ() );

		r.close();
	}
	catch ( Exception e )
	{
		IOFunctions.printlnSafe( "Failed to load metadata for viewsetup=" + view.getViewSetupId() + " timepoint=" + view.getTimePointId() + ": " + e );
		e.printStackTrace();
	}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
protected File getFile( final ViewId view )
{
	final TimePoint tp = sequenceDescription.getTimePoints().getTimePoints().get( view.getTimePointId() );
	final BasicViewSetup  vs = sequenceDescription.getViewSetups().get( view.getViewSetupId() );

	final String timepoint = tp.getName();
	final String angle = vs.getAttribute( Angle.class ).getName();
	final String channel = vs.getAttribute( Channel.class ).getName();
	final String illum = vs.getAttribute( Illumination.class ).getName();

	final String[] fileName = StackList.getFileNamesFor( fileNamePattern, replaceTimepoints, replaceChannels,
			replaceIlluminations, replaceAngles, timepoint, channel, illum, angle,
			numDigitsTimepoints, numDigitsChannels, numDigitsIlluminations, numDigitsAngles );

	// check which of them exists and return it
	for ( final String fn : fileName )
	{
		final File f = new File( path, fn );
		
		if ( f.exists() )
			return f;
		else
			IOFunctions.printlnSafe( "File '" + f.getAbsolutePath() + "' does not exist." );
	}

	IOFunctions.printlnSafe( "Could not find file for tp=" + timepoint + ", angle=" + angle + ", channel=" + channel + ", ill=" + illum );

	return null;
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
@Override
public RandomAccessibleInterval< FloatType > getFloatImage( final ViewId view, final boolean normalize )
{
	try
	{
		final MultipageTiffReader r = new MultipageTiffReader( mmFile );

		final ArrayImg< FloatType, ? > img = ArrayImgs.floats( r.width(), r.height(), r.depth() );
		final BasicViewDescription< ? > vd = sequenceDescription.getViewDescriptions().get( view );

		populateImage( img, vd, r );

		if ( normalize )
			normalize( img );

		updateMetaDataCache( view, r.width(), r.height(), r.depth(), r.calX(), r.calY(), r.calZ() );

		r.close();

		return img;
	}
	catch ( Exception e )
	{
		IOFunctions.printlnSafe( "Failed to load viewsetup=" + view.getViewSetupId() + " timepoint=" + view.getTimePointId() + ": " + e );
		e.printStackTrace();
		return null;
	}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
@Override
public void finalize()
{
	IOFunctions.printlnSafe( "Closing czi: " + cziFile );

	try
	{
		if ( meta != null && meta.getReader() != null )
		{
			meta.getReader().close();
			isClosed = true;
		}
	}
	catch (IOException e) {}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
private void getRGBAndByteDepth( final HashMap< String, Object > map )
{
	try {
		String pixelType = getPixelType();
		rgb_ = pixelType.startsWith("RGB");

		if (pixelType.equals("RGB32") || pixelType.equals("GRAY8")) {
			byteDepth_ = 1;
		} else {
			byteDepth_ = 2;
		}
	} catch (Exception ex) {
		IOFunctions.printlnSafe(ex);
	}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
public Pair< Object, HashMap< String, Object > > readImage( final String label )
{
	if ( indexMap_.containsKey( label ) )
	{
		final FileChannel fileChannel = indexMap_.get( label ).getB();

		if ( fileChannel == null )
		{
			IOFunctions.printlnSafe( "Attempted to read image on FileChannel that is null" );
			return null;
		}

		try
		{
			final long byteOffset = indexMap_.get( label ).getA();

			final IFDData data = readIFD( byteOffset, fileChannel );
			return readTaggedImage( data, fileChannel );
		}
		catch ( IOException ex )
		{
			IOFunctions.printlnSafe(ex);
			return null;
		}
	}
	else
	{
		IOFunctions.printlnSafe( "Exception: label '" + label + "' not in present in hashmap, cannot read data." );
		// label not in map--either writer hasnt finished writing it
		return null;
	}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
private void readIndexMap( final FileChannel fileChannel, final HashMap< String, Pair< Long, FileChannel > > indexMap_ ) throws IOException
{
	final long offset = readOffsetHeaderAndOffset( INDEX_MAP_OFFSET_HEADER, 8, fileChannel );
	final ByteBuffer header = readIntoBuffer( offset, 8, fileChannel );
	if ( header.getInt(0) != INDEX_MAP_HEADER )
		throw new RuntimeException( "Error reading index map header" );

	final int numMappings = header.getInt( 4 );
	final ByteBuffer mapBuffer = readIntoBuffer( offset + 8, 20 * numMappings, fileChannel );
	for ( int i = 0; i < numMappings; ++i )
	{
		final int channel = mapBuffer.getInt( i * 20 );
		final int slice = mapBuffer.getInt( i * 20 + 4 );
		final int frame = mapBuffer.getInt( i * 20 + 8 );
		final int position = mapBuffer.getInt( i * 20 + 12 );
		final long imageOffset = unsignInt( mapBuffer.getInt( i * 20 + 16 ) );
		if ( imageOffset == 0 )
			break; // end of index map reached

		// If a duplicate label is read, forget about the previous one
		// if data has been intentionally overwritten, this gives the most
		// current version
		final String label = generateLabel( channel, slice, frame, position );
		if ( indexMap_.containsKey( label ) )
			IOFunctions.printlnSafe( "ERROR!!! Label: " + label + " already present." );

		//System.out.println( label + " " + getFileForFileChannel( fileChannel ).getName() );

		indexMap_.put( label, new ValuePair< Long, FileChannel >( imageOffset, fileChannel ) );
	}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
private String getString(ByteBuffer buffer) {
	try {
		return new String(buffer.array(), "UTF-8");
	} catch (UnsupportedEncodingException ex) {
		IOFunctions.printlnSafe(ex);
		return "";
	}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
private Pair< Object, HashMap< String, Object > > readTaggedImage( final IFDData data, final FileChannel fileChannel ) throws IOException
{
	final ByteBuffer pixelBuffer = ByteBuffer.allocate( (int)data.bytesPerImage).order( byteOrder_ );
	final ByteBuffer mdBuffer = ByteBuffer.allocate( (int)data.mdLength).order( byteOrder_ );
	fileChannel.read( pixelBuffer, data.pixelOffset );
	fileChannel.read( mdBuffer, data.mdOffset );

	final HashMap< String, Object > md = parseJSONSimple( getString( mdBuffer ) );

	if ( byteDepth_ == 0 )
		getRGBAndByteDepth( md );

	if ( rgb_ )
	{
		IOFunctions.printlnSafe( "RGB types not supported." );
		return null;
	}
	else
	{
		if (byteDepth_ == 1)
		{
			return new ValuePair<Object, HashMap< String, Object >>( pixelBuffer.array(), md );
		}
		else
		{
			final short[] pix = new short[ pixelBuffer.capacity() / 2 ];
			for ( int i = 0; i < pix.length; ++i )
				pix[ i ] = pixelBuffer.getShort( i * 2 );

			return new ValuePair<Object, HashMap< String, Object >>( pix, md );
		}
	}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
public String rotationAngle( final int angleId )
{
	if ( angleId < 0 || angleId >= numAngles() )
	{
		IOFunctions.printlnSafe( "No angle with id " + angleId + ", there are only " + numAngles() + " angles." );
		return String.valueOf( angleId );
	}

	if ( this.angleNames != null )
		return this.angleNames.get( angleId );

	// MVRotations = 0_90_0_90
	// >>> channels increasing, angles increasing faster

	try
	{
		final String ac = summaryMetadata_.get( "MVRotations" ).toString().trim();
		final String[] entries = ac.split( "_" );

		return entries[ angleId ];
	}
	catch ( Exception e )
	{
		IOFunctions.printlnSafe( "Failed to get rotation angle: " + e );
		return "0";
	}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
public static ImagePlus open( File file )
{
	final ImagePlus imp = new Opener().openImage( file.getAbsolutePath() );

	if ( imp == null )
	{
		IOFunctions.printlnSafe( "Could not open file with ImageJ TIFF reader: '" + file.getAbsolutePath() + "'" );
		return null;
	}

	return imp;
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
/**
 * Get {@link FloatType} image normalized to the range [0,1].
 *
 * @param view
 *            timepoint and setup for which to retrieve the image.
 * @param normalize
 * 			  if the image should be normalized to [0,1] or not
 * @return {@link FloatType} image normalized to range [0,1]
 */
@Override
public RandomAccessibleInterval< FloatType > getFloatImage( final ViewId view, final boolean normalize )
{
	final File file = getFile( view );

	if ( file == null )
		throw new RuntimeException( "Could not find file '" + file + "'." );

	IOFunctions.printlnSafe( new Date( System.currentTimeMillis() ) + ": Loading '" + file + "' ..." );

	final ImagePlus imp = open( file );

	if ( imp == null )
		throw new RuntimeException( "Could not load '" + file + "'." );

	final long[] dim = new long[]{ imp.getWidth(), imp.getHeight(), imp.getStack().getSize() };
	final Img< FloatType > img = this.instantiateImg( dim, new FloatType() );

	if ( img == null )
		throw new RuntimeException( "Could not instantiate " + getImgFactory().getClass().getSimpleName() + " for '" + file + "', most likely out of memory." );
	else
		IOFunctions.printlnSafe( new Date( System.currentTimeMillis() ) + ": Opened '" + file + "' [" + dim[ 0 ] + "x" + dim[ 1 ] + "x" + dim[ 2 ] + " image=" + img.getClass().getSimpleName() + "<FloatType>]" );

	imagePlus2ImgLib2Img( imp, img, normalize );

	// update the MetaDataCache of the AbstractImgLoader
	// this does not update the XML ViewSetup but has to be called explicitly before saving
	updateMetaDataCache( view, imp.getWidth(), imp.getHeight(), imp.getStack().getSize(),
			imp.getCalibration().pixelWidth, imp.getCalibration().pixelHeight, imp.getCalibration().pixelDepth );

	imp.close();

	return img;
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
@Override
public void finalize()
{
	IOFunctions.printlnSafe( "Closing sld: " + sldFile );

	try
	{
		if ( meta != null && meta.getReader() != null )
		{
			meta.getReader().close();
			isClosed = true;
		}
	}
	catch (IOException e) {}
}
 

import mpicbg.spim.io.IOFunctions; //導入方法依賴的package包/類
@Override
protected void loadMetaData( final ViewId view )
{
	IOFunctions.printlnSafe( new Date( System.currentTimeMillis() ) + ": Loading metadata for Lightsheet Z1 imgloader not necessary." );
}