Jean-Yves Tinevez tinevez
tinevez
/ gist:7bee36095ed089937c0c55776aa7ad7e
Created
August 25, 2021 14:07
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| Exception in thread "main" java.lang.IllegalArgumentException: Invalid service: net.imagej.legacy.LegacyService | |
| at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:278) | |
| at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:229) | |
| at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:192) | |
| at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:164) | |
| at org.scijava.Context.<init>(Context.java:285) | |
| at org.scijava.Context.<init>(Context.java:234) | |
| at org.scijava.Context.<init>(Context.java:130) | |
| at org.scijava.Context.<init>(Context.java:117) | |
| at org.scijava.Context.<init>(Context.java:106) |
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| public class TestDriveBinningOp | |
| { | |
| @SuppressWarnings( "unchecked" ) | |
| public static < T extends RealType< T > > void main( final String[] args ) throws ClassNotFoundException, InstantiationException, IllegalAccessException, UnsupportedLookAndFeelException, IOException | |
| { | |
| Locale.setDefault( Locale.ROOT ); | |
| UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); | |
| final ImageJ ij = new ImageJ(); | |
| ij.launch( args ); |
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| @Plugin( type = BinningOp.class ) | |
| public class BinningOp< T extends RealType< T > > extends AbstractUnaryFunctionOp< RandomAccessibleInterval< T >, Img< T > > | |
| { | |
| @Parameter( type = ItemIO.INPUT ) | |
| private int[] binfactors; | |
| @Parameter( type = ItemIO.INPUT, required = false ) | |
| private Class< ? extends Op > ocClass = Ops.Stats.Mean.class; |
tinevez
/ MaMuTExportExample.java
Last active
December 28, 2017 16:32
Example of a two way export - reimport of a Model via MaMuT.
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| public static void main( final String[] args ) throws IOException, JDOMException, SpimDataException | |
| { | |
| /* | |
| * 1. Load a regular Mastodon project. | |
| */ | |
| final String bdvFile = "samples/datasethdf5.xml"; | |
| final String modelFile = "samples/model_revised.raw"; | |
| final MamutProject project = new MamutProject( new File( "." ), new File( bdvFile ), new File( modelFile ) ); | |
| final Model model = new Model(); |
tinevez
/ gist:faba62f3ad4b678a21e27eaf9c725365
Created
November 8, 2017 13:25
Hough circle demo error.
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| [ERROR] Exception during event handling: | |
| [Event] org.scijava.module.event.ModulesAddedEvent | |
| context = org.scijava.Context@5386659f | |
| consumed = false | |
| items[0] = class='org.scijava.plugins.commands.io.OpenFile', menu='File > Open Recent > ../../trax-MP-matlab...DH2_CAL_001-1.tif', priority=0.0, enabled=true, pluginType=Command, inputFile='../../trax-MP-matlab/trax-MP-test/2017-1-30_Vu_Sample/DH2_CAL_001-1.tif' | |
| items[1] = class='org.scijava.plugins.commands.io.OpenFile', menu='File > Open Recent > samples/ca-01.lsm', priority=0.0, enabled=true, pluginType=Command, inputFile='samples/ca-01.lsm' | |
| items[2] = class='org.scijava.plugins.commands.io.OpenFile', menu='File > Open Recent > ../../TrackMate/samples/FakeTracks.tif', priority=0.0, enabled=true, pluginType=Command, inputFile='../../TrackMate/samples/FakeTracks.tif' | |
| items[3] = class='org.scijava.plugins.commands.io.OpenFile', menu='File > Open Recent > ...18-6_1.49_100x_zstack_3um_10z_002.tif', priority=0.0, enabled=true, pluginType=Command, inputFile='.. |
tinevez
/ CallTrackMateMultiChannel.py
Created
October 30, 2017 13:44
Fiji Jython script to call TrackMate with the multi-channel analyser extra jar.
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| #@ ImagePlus imp | |
| #@ double (label = "Spot radius", stepSize=0.1) radius | |
| #@ double (label = "Quality threshold") threshold | |
| #@ int (label = "Max frame gap") frameGap | |
| #@ double (label = "Linking max distance") linkingMax | |
| #@ double (label = "Gap-closing max distance") closingMax | |
| # This Python/ImageJ2 script shows how to use TrackMate for multi-channel | |
| # analysis. It is derived from a Groovy script by Jan Eglinger, and uses |