Jean-Yves Tinevez tinevez
tinevez
/ gist:7bee36095ed089937c0c55776aa7ad7e
Created
August 25, 2021 14:07
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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) |
tinevez
/ CallTrackMateMultiChannel.py
Created
October 30, 2017 13:44
Fiji Jython script to call TrackMate with the multi-channel analyser extra jar.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #@ 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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 ); |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| @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.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| [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='.. |