Examples of net.imglib2.transform.integer.MixedTransform

net.imglib2.type.numeric.ARGBType
Mixed transform allows to express common integer view transformations such as translation, rotation, rotoinversion, and projection.
It transform a n-dimensional source vector to a m-dimensional target vector, and can be represented as a m+1 × n+1 homogeneous matrix. The mixed transform can be decomposed as follows:
1. project down (discard some components of the source vector)
2. component permutation
3. component inversion
4. project up (add zero components in the target vector)
5. translation
The project down and component permutation steps are implemented by the {@link #setComponentMapping(int[]) component mapping}. This is a lookup array that specifies for each target dimension from which source dimension it is taken. Note, that it is not allowed to set this array such that a source component is mapped to several target components!
@author Tobias Pietzsch

   */
  public static < T > MixedTransformView< T > addDimension( final RandomAccessible< T > randomAccessible )
  {
    final int m = randomAccessible.numDimensions();
    final int n = m + 1;
    final MixedTransform t = new MixedTransform( n, m );
    return new MixedTransformView< T >( randomAccessible, t );
  }

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  public static < T > MixedTransformView< T > invertAxis( final RandomAccessible< T > randomAccessible, final int d )
  {
    final int n = randomAccessible.numDimensions();
    final boolean[] inv = new boolean[ n ];
    inv[ d ] = true;
    final MixedTransform t = new MixedTransform( n, n );
    t.setComponentInversion( inv );
    return new MixedTransformView< T >( randomAccessible, t );
  }

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    }
    else
    {
      this.source = source;
      final int sourceDim = this.source.numDimensions();
      this.transformToSource = new MixedTransform( n, sourceDim );
      this.transformToSource.set( transformToSource );
    }


    fullViewRandomAccessible = null;
  }

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    {
      System.out.println( "incompatible dimensions" );
      return false;
    }


    final MixedTransform t1t2 = t1.concatenate( t2 );


    final Matrix mt1 = new Matrix( t1.getMatrix() );
    final Matrix mt2 = new Matrix( t2.getMatrix() );
    final Matrix mt1t2 = new Matrix( t1t2.getMatrix() );


    if ( mt1.times( mt2 ).minus( mt1t2 ).normF() > 0.1 )
    {
      System.out.println( "=======================" );
      System.out.println( "t1: " + t1.numSourceDimensions() + " -> " + t1.numTargetDimensions() + " (n -> m)" );
      System.out.println( "t2: " + t2.numSourceDimensions() + " -> " + t2.numTargetDimensions() + " (n -> m)" );
      System.out.println( "t1t2: " + t1t2.numSourceDimensions() + " -> " + t1t2.numTargetDimensions() + " (n -> m)" );


      System.out.print( "t1 = " );
      mt1.print( 1, 0 );
      System.out.print( "t2 = " );
      mt2.print( 1, 0 );

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    {
      System.out.println( "incompatible dimensions" );
      return false;
    }


    final MixedTransform t1t2 = t2.preConcatenate( t1 );


    final Matrix mt1 = new Matrix( t1.getMatrix() );
    final Matrix mt2 = new Matrix( t2.getMatrix() );
    final Matrix mt1t2 = new Matrix( t1t2.getMatrix() );


    if ( mt1.times( mt2 ).minus( mt1t2 ).normF() > 0.1 )
    {
      System.out.println( "=======================" );
      System.out.println( "t1: " + t1.numSourceDimensions() + " -> " + t1.numTargetDimensions() + " (n -> m)" );
      System.out.println( "t2: " + t2.numSourceDimensions() + " -> " + t2.numTargetDimensions() + " (n -> m)" );
      System.out.println( "t1t2: " + t1t2.numSourceDimensions() + " -> " + t1t2.numTargetDimensions() + " (n -> m)" );


      System.out.print( "t1 = " );
      mt1.print( 1, 0 );
      System.out.print( "t2 = " );
      mt2.print( 1, 0 );

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  SlicingTransform slicing1;


  @Before
  public void setUp()
  {
    tr1 = new MixedTransform( 3, 3 );
    long[] translation = new long[] { 3, 4, 5 };
    tr1.setTranslation( translation );


    tr2 = new MixedTransform( 3, 3 );
    translation = new long[] { 7, 8, 9 };
    tr2.setTranslation( translation );


    perm1 = new MixedTransform( 3, 3 );
    boolean[] zero = new boolean[] { false, false, false };
    boolean[] inv = new boolean[] { false, false, false };
    int[] component = new int[] { 0, 2, 1 };
    perm1.setComponentZero( zero );
    perm1.setComponentMapping( component );
    perm1.setComponentInversion( inv );


    rot1 = new MixedTransform( 3, 3 );
    zero = new boolean[] { false, false, false };
    inv = new boolean[] { false, true, false };
    component = new int[] { 1, 0, 2 };
    rot1.setComponentZero( zero );
    rot1.setComponentMapping( component );
    rot1.setComponentInversion( inv );


    proj1 = new MixedTransform( 3, 2 );


    proj2 = new MixedTransform( 2, 3 );


    slice1 = new MixedTransform( 2, 3 );
    slice1.setTranslation( new long[] { 233, 0, 0 } );
    slice1.setComponentMapping( new int[] { 0, 0, 1 } );
    slice1.setComponentZero( new boolean[] { true, false, false } );


    tr3 = new MixedTransform( 2, 2 );
    tr3.setTranslation( new long[] { 10, 10 } );


    comp1 = rot1.concatenate( tr2 );


    translation1 = new TranslationTransform( new long[] { 2011, 3, 24 } );

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        if ( iterableSource.supportsOptimizedCursor( interval ) )
          return new SubInterval( iterableSource );
      }
      else if ( transforms.size() == 1 && SlicingTransform.class.isInstance( transforms.get( 0 ) ) )
      {
        final SlicingTransform t = ( SlicingTransform ) transforms.get( 0 );
        final int m = t.numTargetDimensions();
        final int n = t.numSourceDimensions();


        // Check whether the slicing can be potentially optimized.
        boolean optimizable = true;


        // 1.) Slice dimensions must be mapped to a contiguous range of
        // target dimensions starting with dimension 0.
        int firstZeroDim = 0;
        for ( ; firstZeroDim < m && !t.getComponentZero( firstZeroDim ); ++firstZeroDim );
        for ( int d = firstZeroDim + 1; d < m && optimizable; ++d )
          if ( !t.getComponentZero( d ) )
            optimizable = false;


        // 2.) All slice dimensions must be mapped to a target dimension
        final int[] sourceComponent = new int[ n ];
        if ( optimizable )
        {
          Arrays.fill( sourceComponent, -1 );
          for ( int d = 0; d < m; ++d )
            if ( !t.getComponentZero( d ) )
              sourceComponent[ t.getComponentMapping( d ) ] = d;
          for ( int d = 0; d < n && optimizable; ++d )
            if ( sourceComponent[ d ] < 0 )
              optimizable = false;
        }


        if ( optimizable )
        {
//          System.out.println( "interval = " + Util.printInterval( interval ) );
          final Interval sliceInterval = t.transform( new BoundingBox( interval ) ).getInterval();
//          System.out.println( "transformed interval = " + Util.printInterval( sliceInterval ) );
          if ( iterableSource.supportsOptimizedCursor( sliceInterval ) )
          {
            // check for FlatIterationOrder
            boolean flat = FlatIterationOrder.class.isInstance( iterableSource.subIntervalIterationOrder( sliceInterval ) );

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   * array will update the {@link Image}.
   */
  public ARGBScreenImage( final int width, final int height, final int[] data )
  {
    super( new IntArray( data ), new long[]{ width, height }, new Fraction() );
    setLinkedType( new ARGBType( this ) );
    this.data = data;


    final SampleModel sampleModel = ARGB_COLOR_MODEL.createCompatibleWritableRaster( 1, 1 ).getSampleModel()
        .createCompatibleSampleModel( width, height );
    final DataBuffer dataBuffer = new DataBufferInt( data, width * height, 0 );

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      mapSingle( sourceRandomAccess, currentConverters[ 0 ] );
      return;
    }


    final Cursor< ARGBType > targetCursor = target.localizingCursor();
    final ARGBType bi = new ARGBType();


    while ( targetCursor.hasNext() )
    {
      targetCursor.fwd();
      sourceRandomAccess.setPosition( targetCursor.getLongPosition( 0 ), 0 );
      sourceRandomAccess.setPosition( targetCursor.getLongPosition( 1 ), 1 );
      int aSum = 0, rSum = 0, gSum = 0, bSum = 0;
      for ( int i = 0; i < size; i++ )
      {
        sourceRandomAccess.setPosition( currentPositions[ i ], dimIndex );
        currentConverters[ i ].convert( sourceRandomAccess.get(), bi );


        // accumulate converted result
        final int value = bi.get();
        final int a = ARGBType.alpha( value );
        final int r = ARGBType.red( value );
        final int g = ARGBType.green( value );
        final int b = ARGBType.blue( value );
        aSum += a;

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      sourceRandomAccess.setPosition( currentPositions[ 0 ], dimIndex );
      mapSingle( sourceRandomAccess, currentConverters[ 0 ] );
      return;
    }


    final ARGBType bi = new ARGBType();


    final RandomAccess< ARGBType > targetRandomAccess = target.randomAccess();


    targetRandomAccess.setPosition( min[ 1 ], 1 );
    while ( targetRandomAccess.getLongPosition( 1 ) <= max[ 1 ] )
    {
      sourceRandomAccess.setPosition( min[ 0 ], 0 );
      targetRandomAccess.setPosition( min[ 0 ], 0 );
      while ( targetRandomAccess.getLongPosition( 0 ) <= max[ 0 ] )
      {
        int aSum = 0, rSum = 0, gSum = 0, bSum = 0;
        for ( int i = 0; i < size; i++ )
        {
          sourceRandomAccess.setPosition( currentPositions[ i ], dimIndex );
          currentConverters[ i ].convert( sourceRandomAccess.get(), bi );


          // accumulate converted result
          final int value = bi.get();
          final int a = ARGBType.alpha( value );
          final int r = ARGBType.red( value );
          final int g = ARGBType.green( value );
          final int b = ARGBType.blue( value );
          aSum += a;

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Related Classes of net.imglib2.transform.integer.MixedTransform

Jama.Matrix

net.imglib2.display.ARGBScreenImageExpectationChecking

net.imglib2.display.projector.composite.CompositeXYProjector

net.imglib2.display.projector.composite.CompositeXYRandomAccessibleProjector

net.imglib2.display.screenimage.awt.ARGBScreenImage

net.imglib2.display.screenimage.awt.AWTScreenImageUtil

net.imglib2.FinalInterval

net.imglib2.FlatIterationOrder

net.imglib2.histogram.Histogram1dTest

net.imglib2.histogram.HistogramNdTest

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