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Commit 954b41af authored by Stephan Saalfeld's avatar Stephan Saalfeld
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catmaid and trakem2 average over z

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src/main/java/bdv/BigDataViewer.java
+ 3
− 1
View file @ 954b41af
......@@ -382,8 +382,10 @@ public class BigDataViewer
// final String fn = "/Users/pietzsch/desktop/data/catmaid-confocal.xml";
// final String fn = "/home/saalfeld/openconnectome-bock11-neariso.xml";
// final String fn = "/home/saalfeld/catmaid-confocal.xml";
// final String fn = "/home/saalfeld/catmaid-second-set-tem.xml";
final String fn = "/home/saalfeld/catmaid-l1.xml";
// final String fn = "/home/saalfeld/trakem2-test.xml";
final String fn = "/home/saalfeld/trakem2-fly-test.xml";
// final String fn = "/home/saalfeld/trakem2-fly-test.xml";
// final String fn = "/Users/pietzsch/desktop/data/BDV130418A325/BDV130418A325_NoTempReg.xml";
// final String fn = "/Users/pietzsch/Desktop/data/valia2/valia.xml";
// final String fn = "/Users/pietzsch/workspace/data/fast fly/111010_weber/combined.xml";
......
src/main/java/bdv/img/catmaid/CatmaidImageLoader.java
+ 28
− 25
View file @ 954b41af
......@@ -23,31 +23,23 @@ import bdv.img.cache.VolatileImgCells.CellCache;
public class CatmaidImageLoader extends AbstractViewerImgLoader< ARGBType, VolatileARGBType >
{
private long width;
private String urlFormat;
private long width;
private long height;
private long depth;
private double resXY;
private double resZ;
private String urlFormat;
private int tileWidth;
private int tileHeight;
private int numScales;
private double[][] mipmapResolutions;
private AffineTransform3D[] mipmapTransforms;
private long[][] imageDimensions;
private int[][] blockDimensions;
private double zScale;
private int[] zScales;
private VolatileGlobalCellCache< VolatileIntArray > cache;
......@@ -63,8 +55,10 @@ public class CatmaidImageLoader extends AbstractViewerImgLoader< ARGBType, Volat
height = Long.parseLong( elem.getChildText( "height" ) );
depth = Long.parseLong( elem.getChildText( "depth" ) );
resXY = Double.parseDouble( elem.getChildText( "resXY" ) );
resZ = Double.parseDouble( elem.getChildText( "resZ" ) );
final double resXY = Double.parseDouble( elem.getChildText( "resXY" ) );
final double resZ = Double.parseDouble( elem.getChildText( "resZ" ) );
zScale = resZ / resXY;
urlFormat = elem.getChildText( "urlFormat" );
......@@ -79,25 +73,34 @@ public class CatmaidImageLoader extends AbstractViewerImgLoader< ARGBType, Volat
mipmapResolutions = new double[ numScales ][];
imageDimensions = new long[ numScales ][];
blockDimensions = new int[ numScales ][];
mipmapTransforms = new AffineTransform3D[ numScales ];
zScales = new int[ numScales ];
for ( int l = 0; l < numScales; ++l )
{
mipmapResolutions[ l ] = new double[] { 1 << l, 1 << l, 1 };
imageDimensions[ l ] = new long[] { width >> l, height >> l, depth };
blockDimensions[ l ] = new int[] { tileWidth, tileHeight, 1 };
final int sixy = 1 << l;
int siz = Math.max( 1, ( int )Math.round( sixy / zScale ) );
mipmapResolutions[ l ] = new double[] { sixy, sixy, siz };
imageDimensions[ l ] = new long[] { width >> l, height >> l, depth / siz };
zScales[ l ] = siz;
final AffineTransform3D mipmapTransform = new AffineTransform3D();
mipmapTransform.set( mipmapResolutions[ l ][ 0 ], 0, 0 );
mipmapTransform.set( mipmapResolutions[ l ][ 1 ], 1, 1 );
mipmapTransform.set( 0.5 * ( mipmapResolutions[ l ][ 0 ] - 1 ), 0, 3 );
mipmapTransform.set( 0.5 * ( mipmapResolutions[ l ][ 0 ] - 1 ), 1, 3 );
mipmapTransform.set( sixy, 0, 0 );
mipmapTransform.set( sixy, 1, 1 );
mipmapTransform.set( zScale * siz, 2, 2 );
mipmapTransform.set( 0.5 * ( sixy - 1 ), 0, 3 );
mipmapTransform.set( 0.5 * ( sixy - 1 ), 1, 3 );
mipmapTransform.set( 0.5 * ( zScale * siz - 1 ), 2, 3 );
mipmapTransforms[ l ] = mipmapTransform;
}
final int[] maxLevels = new int[] { numScales - 1 };
cache = new VolatileGlobalCellCache< VolatileIntArray >(
new CatmaidVolatileIntArrayLoader( urlFormat, tileWidth, tileHeight ), 1, 1, numScales, maxLevels, 10 );
new CatmaidVolatileIntArrayLoader( urlFormat, tileWidth, tileHeight, zScales ), 1, 1, numScales, maxLevels, 10 );
}
final static public int getNumScales( long width, long height, final long tileWidth, final long tileHeight )
......@@ -148,7 +151,7 @@ public class CatmaidImageLoader extends AbstractViewerImgLoader< ARGBType, Volat
protected < T extends NativeType< T > > CellImg< T, VolatileIntArray, VolatileCell< VolatileIntArray > > prepareCachedImage( final View view, final int level, final LoadingStrategy loadingStrategy )
{
final long[] dimensions = imageDimensions[ level ];
final int[] cellDimensions = blockDimensions[ level ];
final int[] cellDimensions = new int[]{ tileWidth, tileHeight, 1 };
final CellCache< VolatileIntArray > c = cache.new VolatileCellCache( view.getTimepointIndex(), view.getSetupIndex(), level, loadingStrategy );
final VolatileImgCells< VolatileIntArray > cells = new VolatileImgCells< VolatileIntArray >( c, 1, dimensions, cellDimensions );
......
src/main/java/bdv/img/catmaid/CatmaidVolatileIntArrayLoader.java
+ 64
− 23
View file @ 954b41af
......@@ -14,11 +14,12 @@ public class CatmaidVolatileIntArrayLoader implements CacheArrayLoader< Volatile
{
private VolatileIntArray theEmptyArray;
private final String urlFormat;
final private String urlFormat;
private final int tileWidth;
private final int tileHeight;
final private int tileWidth;
final private int tileHeight;
final private int[] zScales;
/**
* <p>Create a {@link CacheArrayLoader} for a CATMAID source. Tiles are
......@@ -50,12 +51,13 @@ public class CatmaidVolatileIntArrayLoader implements CacheArrayLoader< Volatile
* @param tileWidth
* @param tileHeight
*/
public CatmaidVolatileIntArrayLoader( final String urlFormat, final int tileWidth, final int tileHeight )
public CatmaidVolatileIntArrayLoader( final String urlFormat, final int tileWidth, final int tileHeight, final int[] zScales )
{
theEmptyArray = new VolatileIntArray( tileWidth * tileHeight, false );
this.urlFormat = urlFormat;
this.tileWidth = tileWidth;
this.tileHeight = tileHeight;
this.zScales = zScales;
}
@Override
......@@ -72,37 +74,76 @@ public class CatmaidVolatileIntArrayLoader implements CacheArrayLoader< Volatile
final int[] dimensions,
final long[] min ) throws InterruptedException
{
final int c = ( int ) min[ 0 ] / tileWidth;
final int r = ( int ) min[ 1 ] / tileHeight;
final int col = ( int ) min[ 0 ] / tileWidth;
final int row = ( int ) min[ 1 ] / tileHeight;
final double scale = 1.0 / Math.pow(2.0, level);
final String urlString = String.format( urlFormat, level, scale, min[ 0 ], min[ 1 ], min[ 2 ], tileWidth, tileHeight, r, c );
final int w = dimensions[ 0 ];
final int h = dimensions[ 1 ];
final int[] data = new int[ w * h ];
try
{
final URL url = new URL( urlString );
// final Image image = toolkit.createImage( url );
final BufferedImage jpg = ImageIO.read( url );
/* This gymnastic is necessary to get reproducible gray
* values, just opening a JPG or PNG, even when saved by
* ImageIO, and grabbing its pixels results in gray values
* with a non-matching gamma transfer function, I cannot tell
* why... */
final BufferedImage image = new BufferedImage( w, h, BufferedImage.TYPE_INT_RGB );
image.createGraphics().drawImage( jpg, 0, 0, null );
final PixelGrabber pg = new PixelGrabber( image, 0, 0, w, h, data, 0, w );
pg.grabPixels();
if ( zScales[ level ] > 1 )
{
final long[] rs = new long[ data.length ], gs = new long[ data.length ], bs = new long[ data.length ];
for ( int z = ( int )min[ 2 ] * zScales[ level ], dz = 0; dz < zScales[ level ]; ++dz )
{
final String urlString = String.format( urlFormat, level, scale, min[ 0 ], min[ 1 ], z + dz, tileWidth, tileHeight, row, col );
final URL url = new URL( urlString );
final BufferedImage jpg = ImageIO.read( url );
/* This gymnastic is necessary to get reproducible gray
* values, just opening a JPG or PNG, even when saved by
* ImageIO, and grabbing its pixels results in gray values
* with a non-matching gamma transfer function, I cannot tell
* why... */
final BufferedImage image = new BufferedImage( w, h, BufferedImage.TYPE_INT_RGB );
image.createGraphics().drawImage( jpg, 0, 0, null );
final PixelGrabber pg = new PixelGrabber( image, 0, 0, w, h, data, 0, w );
pg.grabPixels();
for ( int i = 0; i < data.length; ++i )
{
rs[ i ] += ( data[ i ] >> 16 ) & 0xff;
gs[ i ] += ( data[ i ] >> 8 ) & 0xff;
bs[ i ] += data[ i ] & 0xff;
}
}
for ( int i = 0; i < data.length; ++i )
{
final int r = ( int )( rs[ i ] / zScales[ level ] );
final int g = ( int )( gs[ i ] / zScales[ level ] );
final int b = ( int )( bs[ i ] / zScales[ level ] );
data[ i ] = ( ( ( ( r << 8 ) | g ) << 8 ) | b ) | 0xff000000;
}
}
else
{
final String urlString = String.format( urlFormat, level, scale, min[ 0 ], min[ 1 ], min[ 2 ], tileWidth, tileHeight, row, col );
final URL url = new URL( urlString );
// final Image image = toolkit.createImage( url );
final BufferedImage jpg = ImageIO.read( url );
/* This gymnastic is necessary to get reproducible gray
* values, just opening a JPG or PNG, even when saved by
* ImageIO, and grabbing its pixels results in gray values
* with a non-matching gamma transfer function, I cannot tell
* why... */
final BufferedImage image = new BufferedImage( w, h, BufferedImage.TYPE_INT_RGB );
image.createGraphics().drawImage( jpg, 0, 0, null );
final PixelGrabber pg = new PixelGrabber( image, 0, 0, w, h, data, 0, w );
pg.grabPixels();
}
// System.out.println( "success loading r=" + entry.key.r + " c=" + entry.key.c + " url(" + urlString + ")" );
}
catch (final IOException e)
{
System.out.println( "failed loading r=" + r + " c=" + c + " url(" + urlString + ")" );
System.out.println( "failed loading r=" + row + " c=" + col );
}
catch (final InterruptedException e)
{
......
src/main/java/bdv/img/openconnectome/OpenConnectomeImageLoader.java
+ 3
− 1
View file @ 954b41af
......@@ -91,7 +91,9 @@ public class OpenConnectomeImageLoader implements ViewerImgLoader< UnsignedByteT
throws JsonSyntaxException, JsonIOException, IOException
{
final Gson gson = new Gson();
final URL url = new URL( baseUrl + "/" + token + "/info/" );
final String urlString = baseUrl + "/" + token + "/info/";
System.out.println( "Attempting to open " + urlString );
final URL url = new URL( urlString );
return gson.fromJson( new InputStreamReader( url.openStream() ), OpenConnectomeTokenInfo.class );
}
......
src/main/java/bdv/img/trakem2/TrakEM2ImageLoader.java
+ 45
− 29
View file @ 954b41af
......@@ -38,10 +38,10 @@ public class TrakEM2ImageLoader extends AbstractViewerImgLoader< ARGBType, Volat
private int height;
private int depth;
private double zScale;
private int tileWidth;
private int tileHeight;
private double zScale;
private int numScales;
......@@ -51,7 +51,7 @@ public class TrakEM2ImageLoader extends AbstractViewerImgLoader< ARGBType, Volat
private long[][] imageDimensions;
private int[][] blockDimensions;
private int[] zScales;
private VolatileGlobalCellCache< VolatileIntArray > cache;
......@@ -59,14 +59,14 @@ public class TrakEM2ImageLoader extends AbstractViewerImgLoader< ARGBType, Volat
{
super( new ARGBType(), new VolatileARGBType() );
}
@Override
public void init( final Element elem, final File basePath )
public void init( final Project project, final int tileWidth, final int tileHeight, final int numScales )
{
final String projectPath = elem.getChildText( "projectPath" );
this.project = project;
this.tileWidth = tileWidth;
this.tileHeight = tileHeight;
this.numScales = numScales;
ControlWindow.setGUIEnabled( false );
project = Project.openFSProject( projectPath, false);
loader = project.getLoader();
layerset = project.getRootLayerSet();
layerset.setSnapshotsMode(1);
......@@ -79,37 +79,53 @@ public class TrakEM2ImageLoader extends AbstractViewerImgLoader< ARGBType, Volat
final Calibration calibration = layerset.getCalibration();
zScale = calibration.pixelDepth / calibration.pixelWidth;
tileWidth = Integer.parseInt( elem.getChildText( "tileWidth" ) );
tileHeight = Integer.parseInt( elem.getChildText( "tileHeight" ) );
final String numScalesString = elem.getChildText( "numScales" );
if ( numScalesString == null )
numScales = getNumScales( width, height, tileWidth, tileHeight );
else
numScales = Integer.parseInt( numScalesString );
mipmapResolutions = new double[ numScales ][];
imageDimensions = new long[ numScales ][];
blockDimensions = new int[ numScales ][];
mipmapTransforms = new AffineTransform3D[ numScales ];
zScales = new int[ numScales ];
for ( int l = 0; l < numScales; ++l )
{
mipmapResolutions[ l ] = new double[] { 1 << l, 1 << l, 1 };
imageDimensions[ l ] = new long[] { width >> l, height >> l, depth };
blockDimensions[ l ] = new int[] { tileWidth, tileHeight, 1 };
final int sixy = 1 << l;
int siz = Math.max( 1, ( int )Math.round( sixy / zScale ) );
mipmapResolutions[ l ] = new double[] { sixy, sixy, siz };
imageDimensions[ l ] = new long[] { width >> l, height >> l, depth / siz };
zScales[ l ] = siz;
final AffineTransform3D mipmapTransform = new AffineTransform3D();
mipmapTransform.set( mipmapResolutions[ l ][ 0 ], 0, 0 );
mipmapTransform.set( mipmapResolutions[ l ][ 1 ], 1, 1 );
mipmapTransform.set( zScale, 2, 2 );
mipmapTransform.set( 0.5 * ( mipmapResolutions[ l ][ 0 ] - 1 ), 0, 3 );
mipmapTransform.set( 0.5 * ( mipmapResolutions[ l ][ 0 ] - 1 ), 1, 3 );
mipmapTransform.set( sixy, 0, 0 );
mipmapTransform.set( sixy, 1, 1 );
mipmapTransform.set( zScale * siz, 2, 2 );
mipmapTransform.set( 0.5 * ( sixy - 1 ), 0, 3 );
mipmapTransform.set( 0.5 * ( sixy - 1 ), 1, 3 );
mipmapTransform.set( 0.5 * ( zScale * siz - 1 ), 2, 3 );
mipmapTransforms[ l ] = mipmapTransform;
}
final int[] maxLevels = new int[] { numScales - 1 };
cache = new VolatileGlobalCellCache< VolatileIntArray >(
new TrakEM2VolatileIntArrayLoader( loader, layerset ), 1, 1, numScales, maxLevels, 10 );
new TrakEM2VolatileIntArrayLoader( loader, layerset, zScales ), 1, 1, numScales, maxLevels, 10 );
}
@Override
public void init( final Element elem, final File basePath )
{
final String projectPath = elem.getChildText( "projectPath" );
final int tileWidth = Integer.parseInt( elem.getChildText( "tileWidth" ) );
final int tileHeight = Integer.parseInt( elem.getChildText( "tileHeight" ) );
final String numScalesString = elem.getChildText( "numScales" );
if ( numScalesString == null )
numScales = getNumScales( width, height, tileWidth, tileHeight );
else
numScales = Integer.parseInt( numScalesString );
ControlWindow.setGUIEnabled( false );
project = Project.openFSProject( projectPath, false);
init( project, tileWidth, tileHeight, numScales );
}
final static public int getNumScales( long width, long height, final long tileWidth, final long tileHeight )
......@@ -160,7 +176,7 @@ public class TrakEM2ImageLoader extends AbstractViewerImgLoader< ARGBType, Volat
protected < T extends NativeType< T > > CellImg< T, VolatileIntArray, VolatileCell< VolatileIntArray > > prepareCachedImage( final View view, final int level, final LoadingStrategy loadingStrategy )
{
final long[] dimensions = imageDimensions[ level ];
final int[] cellDimensions = blockDimensions[ level ];
final int[] cellDimensions = new int[]{ tileWidth, tileHeight, 1 };
final CellCache< VolatileIntArray > c = cache.new VolatileCellCache( view.getTimepointIndex(), view.getSetupIndex(), level, loadingStrategy );
final VolatileImgCells< VolatileIntArray > cells = new VolatileImgCells< VolatileIntArray >( c, 1, dimensions, cellDimensions );
......
src/main/java/bdv/img/trakem2/TrakEM2VolatileIntArrayLoader.java
+ 59
− 17
View file @ 954b41af
package bdv.img.trakem2;
import ij.ImagePlus;
import ini.trakem2.display.Displayable;
import ini.trakem2.display.LayerSet;
import ini.trakem2.display.Patch;
import ini.trakem2.persistence.Loader;
import java.awt.Color;
......@@ -17,9 +17,11 @@ public class TrakEM2VolatileIntArrayLoader implements CacheArrayLoader< Volatile
{
private VolatileIntArray theEmptyArray;
private final Loader loader;
final private Loader loader;
private final LayerSet layerset;
final private LayerSet layerset;
final private int[] zScales;
/**
* <p>Create a {@link CacheArrayLoader} for a TrakEM2 source. Tiles are
......@@ -29,11 +31,12 @@ public class TrakEM2VolatileIntArrayLoader implements CacheArrayLoader< Volatile
* @param tileWidth
* @param tileHeight
*/
public TrakEM2VolatileIntArrayLoader( final Loader loader, final LayerSet layerset )
public TrakEM2VolatileIntArrayLoader( final Loader loader, final LayerSet layerset, final int[] zScales )
{
theEmptyArray = new VolatileIntArray(1, false );
this.loader = loader;
this.layerset = layerset;
this.zScales = zScales;
}
@Override
......@@ -52,23 +55,62 @@ public class TrakEM2VolatileIntArrayLoader implements CacheArrayLoader< Volatile
{
final int iScale = 1 << level;
final double scale = 1.0 / iScale;
final Rectangle box = new Rectangle( ( int )( min[ 0 ] * iScale ), ( int )( min[ 1 ] * iScale ), dimensions[ 0 ] * iScale, dimensions[ 1 ] * iScale );
final int w = dimensions[ 0 ] * iScale;
final int h = dimensions[ 1 ] * iScale;
final Rectangle box = new Rectangle( ( int )( min[ 0 ] * iScale ), ( int )( min[ 1 ] * iScale ), w, h );
final int[] data = new int[ dimensions[ 0 ] * dimensions[ 1 ] ];
try
{
final Image image = loader.getFlatAWTImage(
layerset.getLayer( ( int )min[ 2 ] ),
box,
scale,
0xffffffff,
ImagePlus.COLOR_RGB,
Patch.class,
null,
true,
new Color( 0x00000000, true ) );
final PixelGrabber pg = new PixelGrabber( image, 0, 0, dimensions[ 0 ], dimensions[ 1 ], data, 0, dimensions[ 0 ] );
pg.grabPixels();
if ( zScales[ level ] > 1 )
{
final long[] rs = new long[ data.length ], gs = new long[ data.length ], bs = new long[ data.length ];
for ( int z = ( int )min[ 2 ] * zScales[ level ], dz = 0; dz < zScales[ level ]; ++dz )
{
final Image image = loader.getFlatAWTImage(
layerset.getLayer( z + dz ),
box,
scale,
0xffffffff,
ImagePlus.COLOR_RGB,
Displayable.class,
null,
true,
new Color( 0x00000000, true ) );
final PixelGrabber pg = new PixelGrabber( image, 0, 0, dimensions[ 0 ], dimensions[ 1 ], data, 0, dimensions[ 0 ] );
pg.grabPixels();
for ( int i = 0; i < data.length; ++i )
{
rs[ i ] += ( data[ i ] >> 16 ) & 0xff;
gs[ i ] += ( data[ i ] >> 8 ) & 0xff;
bs[ i ] += data[ i ] & 0xff;
}
}
for ( int i = 0; i < data.length; ++i )
{
final int r = ( int )( rs[ i ] / zScales[ level ] );
final int g = ( int )( gs[ i ] / zScales[ level ] );
final int b = ( int )( bs[ i ] / zScales[ level ] );
data[ i ] = ( ( ( ( r << 8 ) | g ) << 8 ) | b ) | 0xff000000;
}
}
else
{
final Image image = loader.getFlatAWTImage(
layerset.getLayer( ( int )min[ 2 ] ),
box,
scale,
0xffffffff,
ImagePlus.COLOR_RGB,
Displayable.class,
null,
true,
new Color( 0x00000000, true ) );
final PixelGrabber pg = new PixelGrabber( image, 0, 0, dimensions[ 0 ], dimensions[ 1 ], data, 0, dimensions[ 0 ] );
pg.grabPixels();
}
// System.out.println( "success loading r=" + entry.key.r + " c=" + entry.key.c + " url(" + urlString + ")" );
......
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