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src/main/java/org/janelia/saalfeldlab/hotknife/tools/InpaintMultiSEM.java
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| package org.janelia.saalfeldlab.hotknife.tools; | ||
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| import java.util.ArrayList; | ||
| import java.util.Arrays; | ||
| import java.util.Random; | ||
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| import org.janelia.saalfeldlab.hotknife.InpaintMasked; | ||
| import org.janelia.saalfeldlab.hotknife.SparkSurfaceFit; | ||
| import org.janelia.saalfeldlab.hotknife.util.Util; | ||
| import org.janelia.saalfeldlab.n5.N5FSReader; | ||
| import org.janelia.saalfeldlab.n5.N5Reader; | ||
| import org.janelia.saalfeldlab.n5.imglib2.N5Utils; | ||
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| import ij.ImageJ; | ||
| import ij.ImagePlus; | ||
| import ij.process.FloatProcessor; | ||
| import net.imglib2.Cursor; | ||
| import net.imglib2.FinalInterval; | ||
| import net.imglib2.Interval; | ||
| import net.imglib2.RandomAccess; | ||
| import net.imglib2.RandomAccessibleInterval; | ||
| import net.imglib2.RealLocalizable; | ||
| import net.imglib2.RealPoint; | ||
| import net.imglib2.RealRandomAccess; | ||
| import net.imglib2.cache.img.CachedCellImg; | ||
| import net.imglib2.converter.Converters; | ||
| import net.imglib2.img.Img; | ||
| import net.imglib2.img.array.ArrayImg; | ||
| import net.imglib2.img.array.ArrayImgs; | ||
| import net.imglib2.img.basictypeaccess.array.FloatArray; | ||
| import net.imglib2.img.display.imagej.ImageJFunctions; | ||
| import net.imglib2.interpolation.randomaccess.NLinearInterpolatorFactory; | ||
| import net.imglib2.multithreading.SimpleMultiThreading; | ||
| import net.imglib2.type.numeric.RealType; | ||
| import net.imglib2.type.numeric.integer.UnsignedByteType; | ||
| import net.imglib2.type.numeric.real.FloatType; | ||
| import net.imglib2.util.Intervals; | ||
| import net.imglib2.util.LinAlgHelpers; | ||
| import net.imglib2.view.IntervalView; | ||
| import net.imglib2.view.Views; | ||
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| public class InpaintMultiSEM | ||
| { | ||
| public static boolean isInside( final RealLocalizable p, final Interval r ) | ||
| { | ||
| for ( int d = 0; d < p.numDimensions(); ++d ) | ||
| { | ||
| final double l = p.getDoublePosition( d ); | ||
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| if ( l < r.min( d ) || l > r.max( d ) ) | ||
| return false; | ||
| } | ||
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| return true; | ||
| } | ||
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| public static void inpaint3d( final RandomAccessibleInterval< FloatType > img, final RandomAccessibleInterval< FloatType > out ) | ||
| { | ||
| final Cursor<FloatType> c = Views.iterable( img ).localizingCursor(); | ||
| final RandomAccess< FloatType > o = out.randomAccess(); | ||
| //final RandomAccess< FloatType > i = img.randomAccess(); | ||
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| final int n = img.numDimensions(); | ||
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| //final long[][] distances = new long[ n ][ 2 ]; | ||
| //final float[][] values = new float[ n ][ 2 ]; | ||
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| // random rays being shot out | ||
| final int numOrientations = 256; | ||
| final double p2d = 0.1; | ||
| final Random rnd = new Random( 89656 ); | ||
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| final RealRandomAccess< FloatType > iR = Views.interpolate( Views.extendBorder( img ), new NLinearInterpolatorFactory<>() ).realRandomAccess(); | ||
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| final ArrayList< Long > distances = new ArrayList<>( numOrientations ); | ||
| final ArrayList< Float > values = new ArrayList<>( numOrientations ); | ||
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| final double[] vector = new double[ 3 ]; | ||
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| while ( c.hasNext() ) | ||
| { | ||
| final FloatType v = c.next(); | ||
| o.setPosition( c ); | ||
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| if ( !Float.isNaN( v.get() ) ) | ||
| { | ||
| // no inpainting necessary | ||
| o.get().set( v ); | ||
| } | ||
| else | ||
| { | ||
| //System.out.println( Arrays.toString( o.positionAsLongArray() ) ); | ||
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| values.clear(); | ||
| distances.clear(); | ||
|
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| do | ||
| { | ||
| // get a random direction | ||
| Arrays.fill(vector, 0.0); | ||
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| // limit some to 2d rays | ||
| final int m; | ||
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| if ( n > 2 && rnd.nextDouble() < p2d ) | ||
| m = 2; | ||
| else | ||
| m = n; | ||
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| for ( int d = 0; d < m; ++d ) | ||
| vector[ d ] = rnd.nextDouble() * ( rnd.nextBoolean() ? -1 : 1 ); | ||
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| LinAlgHelpers.normalize( vector ); | ||
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| iR.setPosition( c ); | ||
| long steps = 0; | ||
|
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| do | ||
| { | ||
| iR.move( vector ); | ||
| ++steps; | ||
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| if ( !isInside( iR, img ) ) | ||
| { | ||
| // exited the image boundaries | ||
| break; | ||
| } | ||
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| if ( !Float.isNaN( iR.get().get() ) ) | ||
| { | ||
| // reached the end of the mask | ||
| distances.add( steps ); | ||
| values.add( iR.get().get() ); | ||
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| break; | ||
| } | ||
|
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| } while ( true ); | ||
| } while ( distances.size() < numOrientations ); | ||
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| //System.out.println( Arrays.toString( vector ) + " l=" + LinAlgHelpers.length(vector)); | ||
|
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| // interpolate value | ||
| double sum = 0; | ||
| double sumV = 0; | ||
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| for ( int dir = 0; dir < values.size(); ++dir ) | ||
| { | ||
| double dist = 1.0 / distances.get( dir );//Math.sqrt( Math.sqrt( distances.get( dir ) + 1 ) ); | ||
| //dist = Math.sqrt( dist ); | ||
| //System.out.println( " " + dist + " (" + distances.get( dir ) + ")"); | ||
| sum += dist; | ||
| sumV += values.get( dir ) * dist; | ||
| } | ||
|
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| //System.exit( 0 ); | ||
| final double value = sumV / sum ; | ||
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| o.get().setReal( value ); | ||
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|
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| /* | ||
| // find the nearest pixels in all dim independently, interpolate | ||
| for ( int d = 0; d < n; ++d ) | ||
| { | ||
| // going up | ||
| i.setPosition( c ); | ||
| for ( long l = c.getLongPosition( d ) - 1; l >= img.min( d ); --l ) | ||
| { | ||
| i.setPosition( l, d ); | ||
| if ( !Float.isNaN( i.get().get() ) ) | ||
| { | ||
| // reached the end | ||
| distances[ d ][ 0 ] = c.getLongPosition( d ) - l; | ||
| values[ d ][ 0 ] = i.get().get(); | ||
| break; | ||
| } | ||
| } | ||
| // going down | ||
| i.setPosition( c ); | ||
| for ( long l = c.getLongPosition( d ) + 1; l <= img.max( d ); ++l ) | ||
| { | ||
| i.setPosition( l, d ); | ||
| if ( !Float.isNaN( i.get().get() ) ) | ||
| { | ||
| // reached the end | ||
| distances[ d ][ 1 ] = l - c.getLongPosition( d ); | ||
| values[ d ][ 1 ] = i.get().get(); | ||
| break; | ||
| } | ||
| } | ||
| } | ||
| // interpolate value | ||
| double sum = 0; | ||
| double sumV = 0; | ||
| for ( int d = 0; d < n; ++d ) | ||
| { | ||
| for ( int e = 0; e < distances[ d ].length; ++e ) | ||
| { | ||
| if ( distances[ d ][ e ] > 0 ) | ||
| { | ||
| double dist = 1.0 / distances[ d ][ e ]; | ||
| //dist = Math.sqrt( dist ); | ||
| //System.out.println( " " + d + ": " + dist + " (" + distances[d][e] + ")"); | ||
| sum += dist; | ||
| sumV += values[ d ][ e ] * dist; | ||
| } | ||
| } | ||
| } | ||
| final double value = sumV / sum ; | ||
| o.get().setReal( value ); | ||
| //System.out.println(" " + Arrays.deepToString( distances )); | ||
| //System.out.println(" " + Arrays.deepToString( values )); | ||
| //System.out.println(" " + value ); | ||
| //if ( c.getIntPosition( 0 ) == 160 && c.getIntPosition( 1 ) == 160 ) | ||
| // SimpleMultiThreading.threadHaltUnClean(); | ||
| */ | ||
| } | ||
| } | ||
| } | ||
|
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| public static void main( String[] args ) | ||
| { | ||
| final String n5Path = "/nrs/hess/data/hess_wafer_53/export/hess_wafer_53_center7.n5"; | ||
| final String maskDataset = "/render/slab_000_to_009/s006_m167_align_no35_horiz_avgshd_ic___mask_20240504_144727/s0"; | ||
| final String imageDataset = "/render/slab_000_to_009/s006_m167_align_no35_horiz_avgshd_ic___20240504_085007_norm-layer-clahe/s0"; | ||
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| final N5Reader n5 = new N5FSReader(n5Path); | ||
| final RandomAccessibleInterval< UnsignedByteType > maskRaw = N5Utils.open(n5, maskDataset); | ||
| final RandomAccessibleInterval< UnsignedByteType > imgRaw = N5Utils.open(n5, imageDataset); | ||
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| final Interval interval = Intervals.createMinMax( 32313, 37000, 12, 33808, 37800, 16 ); | ||
| //final Interval interval = Intervals.createMinMax( 32313, 37000, 14, 33808, 37800, 14 ); | ||
| //final Interval interval = Intervals.createMinMax( 32313, 37000, 14, 32540, 37194, 14 ); | ||
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| new ImageJ(); | ||
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| final RandomAccessibleInterval<UnsignedByteType> img = Views.interval( imgRaw , interval ); | ||
| final RandomAccessibleInterval<UnsignedByteType> mask = Views.interval( maskRaw , interval ); | ||
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| ImageJFunctions.show( img ); | ||
| ImageJFunctions.show( mask ); | ||
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| final RandomAccessibleInterval< FloatType > imgF = Views.translate( ArrayImgs.floats( img.dimensionsAsLongArray() ), img.minAsLongArray() ); | ||
| Util.copy( Converters.convert( img, (a,b) -> b.set( a.get() ), new FloatType() ), imgF ); | ||
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| final RandomAccessibleInterval< FloatType > imgOut = Views.translate( ArrayImgs.floats( img.dimensionsAsLongArray() ), img.minAsLongArray() ); | ||
|
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| SparkSurfaceFit.maskSlice(imgF, mask, new FloatType(Float.NaN)); | ||
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| inpaint3d( Views.zeroMin( imgF ), Views.zeroMin( imgOut )); | ||
|
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| ImageJFunctions.show( imgF ); | ||
| ImageJFunctions.show( imgOut ); | ||
| /* | ||
| // 2d code: | ||
| final FloatProcessor fpSlice = Util.materialize( Views.hyperSlice( Views.zeroMin( imgF ), 2, 0 ) ); | ||
| final ArrayImg<FloatType, FloatArray> slice = | ||
| ArrayImgs.floats( | ||
| (float[])fpSlice.getPixels(), | ||
| fpSlice.getWidth(), | ||
| fpSlice.getHeight()); | ||
| SparkSurfaceFit.maskSlice(slice, mask, new FloatType(Float.NaN)); | ||
| InpaintMasked.run(fpSlice); | ||
| new ImagePlus( "img", fpSlice ).show(); | ||
| */ | ||
| /* | ||
| return Views.translate( | ||
| slice, | ||
| Intervals.minAsLongArray(mask));*/ | ||
| } | ||
| } |