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StephanPreibischStephanPreibisch
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moved example code for interest points to src/test
1 parent ed64375 commit 673f10e

3 files changed

Lines changed: 153 additions & 129 deletions

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‎src/main/java/net/preibisch/mvrecon/fiji/spimdata/interestpoints/InterestPointsN5.java‎

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@@ -25,7 +25,6 @@
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import java.io.File;
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import java.net.URI;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
@@ -39,148 +38,20 @@
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import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
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import org.janelia.saalfeldlab.n5.universe.StorageFormat;
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import ij.ImageJ;
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import mpicbg.spim.data.SpimDataException;
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import mpicbg.spim.data.registration.ViewRegistration;
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import mpicbg.spim.data.sequence.MultiResolutionSetupImgLoader;
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import mpicbg.spim.data.sequence.SequenceDescription;
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import mpicbg.spim.data.sequence.SetupImgLoader;
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import mpicbg.spim.data.sequence.ViewDescription;
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import mpicbg.spim.data.sequence.ViewId;
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import net.imglib2.RandomAccess;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.img.display.imagej.ImageJFunctions;
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import net.imglib2.multithreading.SimpleMultiThreading;
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import net.imglib2.position.FunctionRandomAccessible;
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import net.imglib2.realtransform.AffineTransform3D;
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import net.imglib2.type.numeric.integer.UnsignedLongType;
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import net.imglib2.type.numeric.real.DoubleType;
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import net.imglib2.util.Pair;
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import net.imglib2.util.ValuePair;
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import net.imglib2.view.Views;
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import net.preibisch.legacy.io.IOFunctions;
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import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
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import net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2;
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import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
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import util.URITools;
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public class InterestPointsN5 extends InterestPoints
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{
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public static void main( String[] args ) throws SpimDataException
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{
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int viewSetupId = 1;
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//
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// works without the XML, just loads the N5 directly
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//
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InterestPointsN5 ip = new InterestPointsN5(
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URI.create("/nrs/saalfeld/john/for/keller/danio_1_488/dataset-orig-tifs/3/"),
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"tpId_0_viewSetupId_" + viewSetupId + "/beads8v2" );
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List<InterestPoint> points = ip.getInterestPointsCopy();
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for ( final InterestPoint p : points )
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{
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//System.out.println( p.getId() + " " + Arrays.toString( p.getL() ));
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}
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//
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// this needs the XML
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//
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SpimData2 data = new XmlIoSpimData2().load( URI.create("file:/nrs/saalfeld/john/for/keller/danio_1_488/dataset-orig-tifs/3/dataset-stephan.xml") );
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ViewId myViewId = new ViewId( 0, viewSetupId );
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// calibration etc
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SequenceDescription sd = data.getSequenceDescription();
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ViewDescription vd = sd.getViewDescription( myViewId );
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System.out.println( "voxelSize: " + Arrays.toString( vd.getViewSetup().getVoxelSize().dimensionsAsDoubleArray() ) );
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System.out.println( "tile id: " + vd.getViewSetup().getTile().getId() );
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SetupImgLoader<?> setupImgLoader = sd.getImgLoader().getSetupImgLoader( myViewId.getViewSetupId() );
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// full res
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RandomAccessibleInterval<?> img = setupImgLoader.getImage( myViewId.getTimePointId() );
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// multi-res
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if ( MultiResolutionSetupImgLoader.class.isInstance( setupImgLoader ) )
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{
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RandomAccessibleInterval imgS3 = ((MultiResolutionSetupImgLoader)setupImgLoader).getImage( myViewId.getTimePointId(), 3 );
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double[][] mipMapSteps = ((MultiResolutionSetupImgLoader)setupImgLoader).getMipmapResolutions();
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AffineTransform3D[] mipMapT = ((MultiResolutionSetupImgLoader)setupImgLoader).getMipmapTransforms();
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new ImageJ();
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ImageJFunctions.show( imgS3 );
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}
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// dealing with transforms
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Map<ViewId, ViewRegistration> rMap = data.getViewRegistrations().getViewRegistrations();
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ViewRegistration reg = rMap.get( myViewId );
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System.out.println( "num transformations: " + reg.getTransformList().size() );
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reg.updateModel();
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System.out.println( "concatenated model: " + reg.getModel() );
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// dealing with interest points
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Map<ViewId, ViewInterestPointLists> iMap = data.getViewInterestPoints().getViewInterestPoints();
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ViewInterestPointLists iplists = iMap.get( myViewId );
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System.out.println( "\navailable interest point labels:");
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iplists.getHashMap().keySet().forEach( k -> System.out.println( k ) );
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String myLabel = "beads8v2";
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InterestPoints ips = iplists.getInterestPointList( myLabel ); // this is net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5
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// load interest points
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List<InterestPoint> p = ips.getInterestPointsCopy();
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for ( int j = 0; j < 15; ++j )
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{
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InterestPoint point = p.get( j );
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System.out.println( point.getId() + ": " + Arrays.toString( point.getL() ) );
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}
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// load correspondences
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List<CorrespondingInterestPoints> cp = ips.getCorrespondingInterestPointsCopy();
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AffineTransform3D myModel = rMap.get( myViewId ).getModel();
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System.out.println( "\nCorrespondences" );
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for ( int k = 0; k < cp.size(); ++k )
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{
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CorrespondingInterestPoints cpoint = cp.get( k );
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int myId = cpoint.getDetectionId();
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String otherLabel = cpoint.getCorrespodingLabel();
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ViewId otherViewId = cpoint.getCorrespondingViewId();
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int otherId = cpoint.getCorrespondingDetectionId();
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InterestPoint myPoint = p.get( myId );
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InterestPoints pOther = iMap.get( otherViewId ).getInterestPointList( otherLabel );
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InterestPoint otherPoint = pOther.getInterestPointsCopy().get( otherId );
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AffineTransform3D otherModel = rMap.get( otherViewId ).getModel();
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myModel.apply( myPoint.getL(), myPoint.getW() );
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otherModel.apply( otherPoint.getL(), otherPoint.getW() );
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System.out.println(
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Group.pvid( myViewId ) + " label=" + myLabel +" id=" + myId + ", l=" + Arrays.toString( myPoint.getL() ) + " corresponds to " +
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Group.pvid( otherViewId ) + " label=" + otherLabel +" id=" + otherId + ", l=" + Arrays.toString( otherPoint.getL() ) );
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System.out.println( "w=" + Arrays.toString( myPoint.getW() ) + " >>> w=" + Arrays.toString( otherPoint.getW() ) );
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}
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// load and modify all interest points
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iMap.values().forEach( list ->
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{
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list.getHashMap().keySet().forEach( label -> {
175-
list.getInterestPointList( label ).getInterestPointsCopy();
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list.getInterestPointList( label ).getCorrespondingInterestPointsCopy();
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list.getInterestPointList( label ).setBaseDir( URI.create("file:/nrs/saalfeld/john/for/keller/danio_1_488/dataset-orig-tifs/3/test/"));
178-
});
179-
});
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181-
new XmlIoSpimData2().save( data, URI.create("file:/nrs/saalfeld/john/for/keller/danio_1_488/dataset-orig-tifs/3/test/dataset-stephan-2.xml") );
182-
}
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public static int defaultBlockSize = 300_000;
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public static final String baseN5 = "interestpoints.n5";
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‎src/test/java/net/preibisch/mvrecon/fiji/spimdata/interestpoints/ExampleDirectLoading.java‎

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package net.preibisch.mvrecon.fiji.spimdata.interestpoints;
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import java.net.URI;
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import java.util.Arrays;
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import java.util.List;
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7+
import mpicbg.spim.data.SpimDataException;
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9+
public class ExampleDirectLoading
10+
{
11+
public static void main( String[] args ) throws SpimDataException
12+
{
13+
int viewSetupId = 1;
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15+
//
16+
// works without the XML, just loads the N5 directly
17+
//
18+
InterestPointsN5 ip = new InterestPointsN5(
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URI.create("/nrs/saalfeld/john/for/keller/danio_1_488/dataset-orig-tifs/3/"),
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"tpId_0_viewSetupId_" + viewSetupId + "/beads8v2" );
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22+
List<InterestPoint> points = ip.getInterestPointsCopy();
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24+
for ( final InterestPoint p : points )
25+
{
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System.out.println( p.getId() + " " + Arrays.toString( p.getL() ));
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}
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}
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}

‎src/test/java/net/preibisch/mvrecon/fiji/spimdata/interestpoints/ExampleXMLBased.java‎

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package net.preibisch.mvrecon.fiji.spimdata.interestpoints;
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import java.net.URI;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Map;
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import ij.ImageJ;
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import mpicbg.spim.data.SpimDataException;
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import mpicbg.spim.data.registration.ViewRegistration;
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import mpicbg.spim.data.sequence.MultiResolutionSetupImgLoader;
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import mpicbg.spim.data.sequence.SequenceDescription;
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import mpicbg.spim.data.sequence.SetupImgLoader;
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import mpicbg.spim.data.sequence.ViewDescription;
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import mpicbg.spim.data.sequence.ViewId;
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import net.imglib2.RandomAccessibleInterval;
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import net.imglib2.img.display.imagej.ImageJFunctions;
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import net.imglib2.realtransform.AffineTransform3D;
19+
import net.preibisch.mvrecon.fiji.spimdata.SpimData2;
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import net.preibisch.mvrecon.fiji.spimdata.XmlIoSpimData2;
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import net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group;
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public class ExampleXMLBased
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{
25+
public static void main( String[] args ) throws SpimDataException
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{
27+
int viewSetupId = 1;
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//
29+
// this needs the XML
30+
//
31+
SpimData2 data = new XmlIoSpimData2().load( URI.create("file:/nrs/saalfeld/john/for/keller/danio_1_488/dataset-orig-tifs/3/dataset-stephan.xml") );
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33+
ViewId myViewId = new ViewId( 0, viewSetupId );
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// calibration etc
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SequenceDescription sd = data.getSequenceDescription();
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ViewDescription vd = sd.getViewDescription( myViewId );
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System.out.println( "voxelSize: " + Arrays.toString( vd.getViewSetup().getVoxelSize().dimensionsAsDoubleArray() ) );
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System.out.println( "tile id: " + vd.getViewSetup().getTile().getId() );
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SetupImgLoader<?> setupImgLoader = sd.getImgLoader().getSetupImgLoader( myViewId.getViewSetupId() );
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// full res
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RandomAccessibleInterval<?> img = setupImgLoader.getImage( myViewId.getTimePointId() );
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// multi-res
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if ( MultiResolutionSetupImgLoader.class.isInstance( setupImgLoader ) )
48+
{
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RandomAccessibleInterval imgS3 = ((MultiResolutionSetupImgLoader)setupImgLoader).getImage( myViewId.getTimePointId(), 3 );
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double[][] mipMapSteps = ((MultiResolutionSetupImgLoader)setupImgLoader).getMipmapResolutions();
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AffineTransform3D[] mipMapT = ((MultiResolutionSetupImgLoader)setupImgLoader).getMipmapTransforms();
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new ImageJ();
53+
ImageJFunctions.show( imgS3 );
54+
}
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56+
// dealing with transforms
57+
Map<ViewId, ViewRegistration> rMap = data.getViewRegistrations().getViewRegistrations();
58+
ViewRegistration reg = rMap.get( myViewId );
59+
System.out.println( "num transformations: " + reg.getTransformList().size() );
60+
reg.updateModel();
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System.out.println( "concatenated model: " + reg.getModel() );
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// dealing with interest points
64+
Map<ViewId, ViewInterestPointLists> iMap = data.getViewInterestPoints().getViewInterestPoints();
65+
ViewInterestPointLists iplists = iMap.get( myViewId );
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67+
System.out.println( "\navailable interest point labels:");
68+
iplists.getHashMap().keySet().forEach( k -> System.out.println( k ) );
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String myLabel = "beads8v2";
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InterestPoints ips = iplists.getInterestPointList( myLabel ); // this is net.preibisch.mvrecon.fiji.spimdata.interestpoints.InterestPointsN5
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// load interest points
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List<InterestPoint> p = ips.getInterestPointsCopy();
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75+
for ( int j = 0; j < Math.min( 15, p.size() ) ; ++j )
76+
{
77+
InterestPoint point = p.get( j );
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System.out.println( point.getId() + ": " + Arrays.toString( point.getL() ) );
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}
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81+
// load correspondences
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List<CorrespondingInterestPoints> cp = ips.getCorrespondingInterestPointsCopy();
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84+
AffineTransform3D myModel = rMap.get( myViewId ).getModel();
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System.out.println( "\nCorrespondences" );
87+
for ( int k = 0; k < cp.size(); ++k )
88+
{
89+
CorrespondingInterestPoints cpoint = cp.get( k );
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91+
int myId = cpoint.getDetectionId();
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String otherLabel = cpoint.getCorrespodingLabel();
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ViewId otherViewId = cpoint.getCorrespondingViewId();
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int otherId = cpoint.getCorrespondingDetectionId();
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96+
InterestPoint myPoint = p.get( myId );
97+
98+
InterestPoints pOther = iMap.get( otherViewId ).getInterestPointList( otherLabel );
99+
InterestPoint otherPoint = pOther.getInterestPointsCopy().get( otherId );
100+
AffineTransform3D otherModel = rMap.get( otherViewId ).getModel();
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102+
myModel.apply( myPoint.getL(), myPoint.getW() );
103+
otherModel.apply( otherPoint.getL(), otherPoint.getW() );
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System.out.println(
106+
Group.pvid( myViewId ) + " label=" + myLabel +" id=" + myId + ", l=" + Arrays.toString( myPoint.getL() ) + " corresponds to " +
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Group.pvid( otherViewId ) + " label=" + otherLabel +" id=" + otherId + ", l=" + Arrays.toString( otherPoint.getL() ) );
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System.out.println( "w=" + Arrays.toString( myPoint.getW() ) + " >>> w=" + Arrays.toString( otherPoint.getW() ) );
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}
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// load and modify all interest points
113+
iMap.values().forEach( list ->
114+
{
115+
list.getHashMap().keySet().forEach( label -> {
116+
list.getInterestPointList( label ).getInterestPointsCopy();
117+
list.getInterestPointList( label ).getCorrespondingInterestPointsCopy();
118+
list.getInterestPointList( label ).setBaseDir( URI.create("file:/nrs/saalfeld/john/for/keller/danio_1_488/dataset-orig-tifs/3/test/"));
119+
});
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});
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new XmlIoSpimData2().save( data, URI.create("file:/nrs/saalfeld/john/for/keller/danio_1_488/dataset-orig-tifs/3/test/dataset-stephan-2.xml") );
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}
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}

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