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feat: bounding box estimation for RealTransformed RealIntervals (#37)
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* feat: bounding box estimation for RealTransformed RealIntervals

default implementation in RealTransform with extensible interface for
sampling method
override trivial cases in Translations, scales, and affine transformations

---------

Co-authored-by: Stephan Saalfeld <[email protected]>
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@bogovicj @axtimwalde
bogovicj and axtimwalde authored Jun 15, 2024
1 parent a62d90a commit ce8f984
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Showing 14 changed files with 990 additions and 34 deletions.
26 changes: 17 additions & 9 deletions src/main/java/net/imglib2/realtransform/AbstractAffineTransform.java
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Expand Up @@ -11,13 +11,13 @@
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
Expand All @@ -34,17 +34,19 @@

package net.imglib2.realtransform;

import Jama.Matrix;
import net.imglib2.RealInterval;
import net.imglib2.RealLocalizable;
import net.imglib2.RealPoint;
import net.imglib2.RealPositionable;
import Jama.Matrix;
import net.imglib2.realtransform.interval.IntervalSamplingMethod;

/**
* An abstract implementation of an affine transformation that returns default
* values referring to the identity transformation for all fields. This
* implementation is not thread safe. Create a {@link #copy()} for each
* consumer.
*
*
* @author Stephan Saalfeld
*/
public abstract class AbstractAffineTransform implements AffineGet, AffineSet
Expand Down Expand Up @@ -136,7 +138,7 @@ public int numTargetDimensions()
{
return n;
}

@Override
public void apply( final double[] source, final double[] target )
{
Expand All @@ -148,11 +150,11 @@ public void apply( final double[] source, final double[] target )
for ( int c = 0; c < n; ++c )
tmp[ r ] += source[ c ] * a.get( r, c );
}

for ( int r = 0; r < n; ++r )
target[ r ] = tmp[ r ] + t[ r ];
}

@Override
public void apply( final float[] source, final float[] target )
{
Expand All @@ -164,7 +166,7 @@ public void apply( final float[] source, final float[] target )
for ( int c = 0; c < n; ++c )
tmp[ r ] += source[ c ] * a.get( r, c );
}

for ( int r = 0; r < n; ++r )
target[ r ] = ( float )( tmp[ r ] + t[ r ] );
}
Expand All @@ -180,7 +182,7 @@ public void apply( final RealLocalizable source, final RealPositionable target )
for ( int c = 0; c < n; ++c )
tmp[ r ] += source.getDoublePosition( c ) * a.get( r, c );
}

for ( int r = 0; r < n; ++r )
target.setPosition( tmp[ r ] + t[ r ], r );
}
Expand Down Expand Up @@ -215,4 +217,10 @@ public RealLocalizable d( final int d )

return ds[ d ];
}

@Override
public RealInterval boundingInterval( final RealInterval interval, final IntervalSamplingMethod samplingMethdod )
{
return AffineGet.super.boundingInterval( interval, IntervalSamplingMethod.CORNERS );
}
}
52 changes: 37 additions & 15 deletions src/main/java/net/imglib2/realtransform/AbstractScale.java
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Expand Up @@ -11,13 +11,13 @@
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
Expand All @@ -34,9 +34,12 @@

package net.imglib2.realtransform;

import net.imglib2.FinalRealInterval;
import net.imglib2.RealInterval;
import net.imglib2.RealLocalizable;
import net.imglib2.RealPoint;
import net.imglib2.RealPositionable;
import net.imglib2.realtransform.interval.IntervalSamplingMethod;

/**
* <em>n</em>-d arbitrary scaling. Abstract base implementation.
Expand All @@ -63,7 +66,7 @@ public AbstractScale( final double... s )

/**
* Set the scale vector.
*
*
* @param s
* s.length &lt;= the number of dimensions of this
* {@link AbstractScale}
Expand All @@ -74,7 +77,7 @@ public AbstractScale( final double... s )
public void applyInverse( final double[] source, final double[] target )
{
assert source.length >= s.length && target.length >= s.length : "Input dimensions too small.";

for ( int d = 0; d < s.length; ++d )
source[ d ] = target[ d ] / s[ d ];
}
Expand All @@ -83,17 +86,17 @@ public void applyInverse( final double[] source, final double[] target )
public void applyInverse( final float[] source, final float[] target )
{
assert source.length >= s.length && target.length >= s.length : "Input dimensions too small.";

for ( int d = 0; d < s.length; ++d )
source[ d ] = ( float )( target[ d ] / s[ d ] );

}

@Override
public void applyInverse( final RealPositionable source, final RealLocalizable target )
{
assert source.numDimensions() >= s.length && target.numDimensions() >= s.length : "Input dimensions too small.";

for ( int d = 0; d < s.length; ++d )
source.setPosition( target.getDoublePosition( d ) / s[ d ], d );
}
Expand Down Expand Up @@ -123,7 +126,7 @@ public int numTargetDimensions()
public void apply( final double[] source, final double[] target )
{
assert source.length >= s.length && target.length >= s.length : "Input dimensions too small.";

for ( int d = 0; d < s.length; ++d )
target[ d ] = source[ d ] * s[ d ];
}
Expand All @@ -132,7 +135,7 @@ public void apply( final double[] source, final double[] target )
public void apply( final float[] source, final float[] target )
{
assert source.length >= s.length && target.length >= s.length : "Input dimensions too small.";

for ( int d = 0; d < s.length; ++d )
target[ d ] = ( float )( source[ d ] * s[ d ] );
}
Expand All @@ -141,7 +144,7 @@ public void apply( final float[] source, final float[] target )
public void apply( final RealLocalizable source, final RealPositionable target )
{
assert source.numDimensions() >= s.length && target.numDimensions() >= s.length : "Input dimensions too small.";

for ( int d = 0; d < s.length; ++d )
target.setPosition( source.getDoublePosition( d ) * s[ d ], d );
}
Expand All @@ -150,7 +153,7 @@ public void apply( final RealLocalizable source, final RealPositionable target )
public double get( final int row, final int column )
{
assert row >= 0 && row < numDimensions() : "Dimension index out of bounds.";

return row == column ? s[ row ] : 0;
}

Expand All @@ -168,7 +171,7 @@ public double[] getRowPackedCopy()
public RealLocalizable d( final int d )
{
assert d >= 0 && d < numDimensions() : "Dimension index out of bounds.";

return ds[ d ];
}

Expand All @@ -186,14 +189,33 @@ public double[] getScaleCopy()
{
return s.clone();
}

@Override
public double getTranslation( final int d ) {
public double getTranslation( final int d )
{
return 0.0;
}

@Override
public double[] getTranslationCopy() {
public double[] getTranslationCopy()
{
return new double[ s.length ];
}

@Override
public RealInterval boundingInterval( final RealInterval interval, final IntervalSamplingMethod samplingMethdod )
{
assert interval.numDimensions() >= s.length : "Interval does not have enough dimensions.";

final double[] min = interval.minAsDoubleArray();
final double[] max = interval.maxAsDoubleArray();

for ( int d = 0; d < s.length; ++d )
{
min[ d ] *= s[ d ];
max[ d ] *= s[ d ];
}

return new FinalRealInterval( min, max, false );
}
}
32 changes: 26 additions & 6 deletions src/main/java/net/imglib2/realtransform/AbstractTranslation.java
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Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,13 @@
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
Expand All @@ -34,13 +34,16 @@

package net.imglib2.realtransform;

import net.imglib2.FinalRealInterval;
import net.imglib2.RealInterval;
import net.imglib2.RealLocalizable;
import net.imglib2.RealPoint;
import net.imglib2.RealPositionable;
import net.imglib2.realtransform.interval.IntervalSamplingMethod;

/**
* <em>n</em>-d translation. Abstract base implementation.
*
*
* @author Stephan Saalfeld
*/
abstract public class AbstractTranslation implements TranslationGet
Expand Down Expand Up @@ -77,7 +80,7 @@ public AbstractTranslation( final double... t )

/**
* Set the translation vector.
*
*
* @param t
* t.length &lt;= the number of dimensions of this
* {@link AbstractTranslation}
Expand All @@ -86,7 +89,7 @@ public AbstractTranslation( final double... t )

/**
* Set one value of the translation vector.
*
*
* @param t
* t.length &lt;= the number of dimensions of this
* {@link AbstractTranslation}
Expand Down Expand Up @@ -197,7 +200,7 @@ public RealLocalizable d( final int d )

return ds[ d ];
}

@Override
public double getScale( final int d ) {
return 0.0;
Expand All @@ -224,4 +227,21 @@ public double[] getTranslationCopy()

@Override
abstract public AbstractTranslation inverse();

@Override
public RealInterval boundingInterval( final RealInterval interval, final IntervalSamplingMethod samplingMethdod )
{
assert interval.numDimensions() >= t.length : "Interval does not have enough dimensions.";

final double[] min = interval.minAsDoubleArray();
final double[] max = interval.maxAsDoubleArray();

for ( int d = 0; d < t.length; ++d )
{
min[ d ] += t[ d ];
max[ d ] += t[ d ];
}

return new FinalRealInterval( min, max, false );
}
}
24 changes: 24 additions & 0 deletions src/main/java/net/imglib2/realtransform/RealTransform.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,9 +34,11 @@

package net.imglib2.realtransform;

import net.imglib2.RealInterval;
import net.imglib2.RealLocalizable;
import net.imglib2.RealPoint;
import net.imglib2.RealPositionable;
import net.imglib2.realtransform.interval.IntervalSamplingMethod;

/**
* Transformation from R<sup><em>n</em></sup> to R<sup><em>m</em></sup>.
Expand Down Expand Up @@ -257,4 +259,26 @@ default boolean isIdentity()
{
return false;
}

/**
* Estimate the {@link RealInterval} that bounds the given RealInterval
* after being transformed by a {@link RealTransform}.
* <p>
* For arbitrary transformations, it is not necessarily possible to
* directly calculate the resulting bounding box trivially, therefore,
* a sampling methods for coordinates in the source interval must be
* provided. {@link RealTransform}s that can calculate the bounding
* interval more efficiently than by sampling coordinates are encouraged
* to override this method and to ignore the provided sampling method.
*
* @param interval
* the real interval
* @param samplingMethod
* the method used to sample coordinates of the source interval
* @return the bounding interval
*/
default RealInterval boundingInterval( final RealInterval interval, final IntervalSamplingMethod samplingMethod )
{
return samplingMethod.bounds( interval, this );
}
}
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