From 0d14629436cb5dcb40faf24d2d423121ee809b76 Mon Sep 17 00:00:00 2001 From: Jean-Yves Tinevez Date: Mon, 17 Apr 2023 20:21:15 +0200 Subject: [PATCH 01/13] Update parent to pom-scijava v34.1.0 --- pom.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pom.xml b/pom.xml index e91d00a..9f6fee6 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ org.scijava pom-scijava - 34.0.0 + 34.1.0 From 957aad434204879e86bd0a659d98ca5d8c4275a0 Mon Sep 17 00:00:00 2001 From: Jean-Yves Tinevez Date: Mon, 17 Apr 2023 20:21:51 +0200 Subject: [PATCH 02/13] Temporary coupling to TrackMate v8.0.0-SNAPSHOT --- pom.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/pom.xml b/pom.xml index 9f6fee6..d663b3c 100644 --- a/pom.xml +++ b/pom.xml @@ -93,6 +93,7 @@ sc.fiji TrackMate + 8.0.0-SNAPSHOT From 30a60d392471cfada6c293f9f135a8c3c3e4af58 Mon Sep 17 00:00:00 2001 From: Jean-Yves Tinevez Date: Mon, 17 Apr 2023 20:44:12 +0200 Subject: [PATCH 03/13] Support 3D segmentation with WEKA. --- .../trackmate/weka/WekaDetectorFactory.java | 7 ++-- .../plugin/trackmate/weka/WekaRunner.java | 37 ++++++------------- 2 files changed, 15 insertions(+), 29 deletions(-) diff --git a/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java b/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java index 568f583..29546a0 100644 --- a/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java +++ b/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java @@ -8,12 +8,12 @@ * it under the terms of the GNU General Public License as * published by the Free Software Foundation, either version 3 of the * License, or (at your option) any later version. - * + * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. - * + * * You should have received a copy of the GNU General Public * License along with this program. If not, see * . @@ -92,7 +92,8 @@ public class WekaDetectorFactory< T extends RealType< T > & NativeType< T > > im public static final String INFO_TEXT = "" + "This detector relies on the 'Trainable Weka segmentation' plugin to detect objects." + "

" - + "It works for 2D and 3D images, but returns contours only for 2D images." + + "It works for 2D and 3D images, returns contours for 2D images and meshes" + + "for 3D images." + "

" + "You need to provide the path to a classifier previously trained and saved using the " + "'Trainable Weka segmentation' plugin. It will classically be a '.model' file. " diff --git a/src/main/java/fiji/plugin/trackmate/weka/WekaRunner.java b/src/main/java/fiji/plugin/trackmate/weka/WekaRunner.java index c434126..52618f6 100644 --- a/src/main/java/fiji/plugin/trackmate/weka/WekaRunner.java +++ b/src/main/java/fiji/plugin/trackmate/weka/WekaRunner.java @@ -8,12 +8,12 @@ * it under the terms of the GNU General Public License as * published by the Free Software Foundation, either version 3 of the * License, or (at your option) any later version. - * + * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. - * + * * You should have received a copy of the GNU General Public * License along with this program. If not, see * . @@ -174,7 +174,7 @@ public List< Spot > getSpotsFromLastProbabilities( final double threshold, final /** * Exposes the last probability image calculated. - * + * * @return the last probability image calculated. May be null */ public RandomAccessibleInterval< T > getLastOutput() @@ -184,29 +184,14 @@ public RandomAccessibleInterval< T > getLastOutput() public List< Spot > getSpots( final RandomAccessibleInterval< T > proba, final double[] calibration, final double threshold, final boolean simplify ) { - final List< Spot > spots; - if ( isProcessing3D ) - { - spots = MaskUtils.fromThreshold( - proba, - proba, - calibration, - threshold, - numThreads, - proba ); - } - else - { - spots = MaskUtils.fromThresholdWithROI( - proba, - proba, - calibration, - threshold, - simplify, - numThreads, - proba ); - } - return spots; + return MaskUtils.fromThresholdWithROI( + proba, + proba, + calibration, + threshold, + simplify, + numThreads, + proba ); } private RandomAccessibleInterval< T > deinterleave( final RandomAccessibleInterval< T > proba, final long start, final long step ) From b838aa570489008f160ab5f2ca0c2e5e9fe7966e Mon Sep 17 00:00:00 2001 From: Jean-Yves Tinevez Date: Mon, 17 Apr 2023 20:44:20 +0200 Subject: [PATCH 04/13] Update interactive test. --- .../plugin/trackmate/weka/TrackMateWeka3DTestDrive.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/test/java/fiji/plugin/trackmate/weka/TrackMateWeka3DTestDrive.java b/src/test/java/fiji/plugin/trackmate/weka/TrackMateWeka3DTestDrive.java index 189e0cd..ea5d71a 100644 --- a/src/test/java/fiji/plugin/trackmate/weka/TrackMateWeka3DTestDrive.java +++ b/src/test/java/fiji/plugin/trackmate/weka/TrackMateWeka3DTestDrive.java @@ -8,12 +8,12 @@ * it under the terms of the GNU General Public License as * published by the Free Software Foundation, either version 3 of the * License, or (at your option) any later version. - * + * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. - * + * * You should have received a copy of the GNU General Public * License along with this program. If not, see * . @@ -37,7 +37,8 @@ public static void main( final String[] args ) throws IOException, ClassNotFound { UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); ImageJ.main( args ); - final String path = "samples/merged.tif"; +// final String path = "samples/merged.tif"; + final String path = "samples/mesh/CElegansMask3D.tif"; IJ.openImage( path ).show(); new TrackMatePlugIn().run( null ); } From f5329aceb1b8aa8ee331704ce5387287a741a0ce Mon Sep 17 00:00:00 2001 From: Jean-Yves Tinevez Date: Wed, 29 Nov 2023 18:32:47 +0100 Subject: [PATCH 05/13] Update parent-pom to scijava v37.0.0 --- pom.xml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/pom.xml b/pom.xml index d663b3c..7d314f9 100644 --- a/pom.xml +++ b/pom.xml @@ -5,7 +5,7 @@ org.scijava pom-scijava - 34.1.0 + 37.0.0 @@ -86,14 +86,13 @@ 0.11.1 - 7.10.2 + 8.0.0-SNAPSHOT sc.fiji TrackMate - 8.0.0-SNAPSHOT From 25b00928c045d276884604277a6b5570887081a3 Mon Sep 17 00:00:00 2001 From: Jean-Yves Tinevez Date: Wed, 29 Nov 2023 18:33:11 +0100 Subject: [PATCH 06/13] Fix missing smoothing scale. But right now we default to not smooth anything, as before. --- .../plugin/trackmate/weka/WekaDetectionPreviewer.java | 8 ++++++-- .../java/fiji/plugin/trackmate/weka/WekaDetector.java | 8 ++++++-- .../fiji/plugin/trackmate/weka/WekaDetectorFactory.java | 8 +++++++- src/main/java/fiji/plugin/trackmate/weka/WekaRunner.java | 7 ++++--- .../java/fiji/plugin/trackmate/weka/WekaTestDrive.java | 6 +++--- 5 files changed, 26 insertions(+), 11 deletions(-) diff --git a/src/main/java/fiji/plugin/trackmate/weka/WekaDetectionPreviewer.java b/src/main/java/fiji/plugin/trackmate/weka/WekaDetectionPreviewer.java index 45b6234..92852f5 100644 --- a/src/main/java/fiji/plugin/trackmate/weka/WekaDetectionPreviewer.java +++ b/src/main/java/fiji/plugin/trackmate/weka/WekaDetectionPreviewer.java @@ -22,6 +22,7 @@ package fiji.plugin.trackmate.weka; import static fiji.plugin.trackmate.detection.DetectorKeys.KEY_TARGET_CHANNEL; +import static fiji.plugin.trackmate.detection.ThresholdDetectorFactory.KEY_SMOOTHING_SCALE; import static fiji.plugin.trackmate.weka.WekaDetectorFactory.KEY_CLASSIFIER_FILEPATH; import static fiji.plugin.trackmate.weka.WekaDetectorFactory.KEY_CLASS_INDEX; import static fiji.plugin.trackmate.weka.WekaDetectorFactory.KEY_PROBA_THRESHOLD; @@ -108,13 +109,16 @@ protected Pair< Model, Double > runPreviewDetection( */ final Map< String, Object > dsettings = new HashMap<>( detectorSettings ); - @SuppressWarnings( "unchecked" ) final ImgPlus< T > img = TMUtils.rawWraps( settings.imp ); final int channel = ( Integer ) dsettings.get( KEY_TARGET_CHANNEL ) - 1; final ImgPlus< T > input = TMUtils.hyperSlice( img, channel, frame ); final int classIndex = ( Integer ) dsettings.get( KEY_CLASS_INDEX ); final double probaThreshold = ( Double ) dsettings.get( KEY_PROBA_THRESHOLD ); final boolean simplify = true; + final Object smoothingObj = dsettings.get( KEY_SMOOTHING_SCALE ); + final double smoothingScale = smoothingObj == null + ? -1. + : ( ( Number ) smoothingObj ).doubleValue(); final boolean is3D = input.dimensionIndex( Axes.Z ) >= 0; // First test to make sure we can read the classifier file. @@ -180,7 +184,7 @@ protected Pair< Model, Double > runPreviewDetection( } logger.log( "Creating spots from probabilities." ); - final List< Spot > spots = wekaRunner.getSpotsFromLastProbabilities( probaThreshold, simplify ); + final List< Spot > spots = wekaRunner.getSpotsFromLastProbabilities( probaThreshold, simplify, smoothingScale ); if ( spots == null ) { logger.error( "Problem creating spots: " + wekaRunner.getErrorMessage() ); diff --git a/src/main/java/fiji/plugin/trackmate/weka/WekaDetector.java b/src/main/java/fiji/plugin/trackmate/weka/WekaDetector.java index f832d1a..f4f08d5 100644 --- a/src/main/java/fiji/plugin/trackmate/weka/WekaDetector.java +++ b/src/main/java/fiji/plugin/trackmate/weka/WekaDetector.java @@ -59,13 +59,16 @@ public class WekaDetector< T extends RealType< T > & NativeType< T > > implement private final boolean simplify; + private final double smoothingScale; + public WekaDetector( final WekaRunner< T > runner, final ImgPlus< T > img, final Interval interval, final int classIndex, final double probaThreshold, - final boolean simplify ) + final boolean simplify, + final double smoothingScale ) { this.runner = runner; this.img = img; @@ -73,6 +76,7 @@ public WekaDetector( this.classIndex = classIndex; this.probaThreshold = probaThreshold; this.simplify = simplify; + this.smoothingScale = smoothingScale; this.baseErrorMessage = BASE_ERROR_MESSAGE; } @@ -99,7 +103,7 @@ public boolean process() return false; } - spots = runner.getSpots( probabilities, TMUtils.getSpatialCalibration( img ), probaThreshold, simplify ); + spots = runner.getSpots( probabilities, TMUtils.getSpatialCalibration( img ), probaThreshold, simplify, smoothingScale ); if ( spots == null ) { System.err.println( "Problem creating spots: " + runner.getErrorMessage() ); diff --git a/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java b/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java index 29546a0..e970dbb 100644 --- a/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java +++ b/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java @@ -23,6 +23,7 @@ import static fiji.plugin.trackmate.detection.DetectorKeys.DEFAULT_TARGET_CHANNEL; import static fiji.plugin.trackmate.detection.DetectorKeys.KEY_TARGET_CHANNEL; +import static fiji.plugin.trackmate.detection.ThresholdDetectorFactory.KEY_SMOOTHING_SCALE; import static fiji.plugin.trackmate.io.IOUtils.readDoubleAttribute; import static fiji.plugin.trackmate.io.IOUtils.readIntegerAttribute; import static fiji.plugin.trackmate.io.IOUtils.readStringAttribute; @@ -133,13 +134,18 @@ public SpotDetector< T > getDetector( final Interval interval, final int frame ) final int classIndex = ( Integer ) settings.get( KEY_CLASS_INDEX ); final double probaThreshold = ( Double ) settings.get( KEY_PROBA_THRESHOLD ); final boolean simplify = true; + final Object smoothingObj = settings.get( KEY_SMOOTHING_SCALE ); + final double smoothingScale = smoothingObj == null + ? -1. + : ( ( Number ) smoothingObj ).doubleValue(); final WekaDetector< T > detector = new WekaDetector<>( runner, input, interval, classIndex, probaThreshold, - simplify ); + simplify, + smoothingScale ); return detector; } diff --git a/src/main/java/fiji/plugin/trackmate/weka/WekaRunner.java b/src/main/java/fiji/plugin/trackmate/weka/WekaRunner.java index 52618f6..1a40dec 100644 --- a/src/main/java/fiji/plugin/trackmate/weka/WekaRunner.java +++ b/src/main/java/fiji/plugin/trackmate/weka/WekaRunner.java @@ -156,7 +156,7 @@ public RandomAccessibleInterval< T > computeProbabilities( return output; } - public List< Spot > getSpotsFromLastProbabilities( final double threshold, final boolean simplify ) + public List< Spot > getSpotsFromLastProbabilities( final double threshold, final boolean simplify, final double smoothingScale ) { errorMessage = null; if ( segmentation == null ) @@ -169,7 +169,7 @@ public List< Spot > getSpotsFromLastProbabilities( final double threshold, final errorMessage = "Probabilities have not been computed yet."; return null; } - return getSpots( lastOutput, lastCalibration, threshold, simplify ); + return getSpots( lastOutput, lastCalibration, threshold, simplify, smoothingScale ); } /** @@ -182,7 +182,7 @@ public RandomAccessibleInterval< T > getLastOutput() return lastOutput; } - public List< Spot > getSpots( final RandomAccessibleInterval< T > proba, final double[] calibration, final double threshold, final boolean simplify ) + public List< Spot > getSpots( final RandomAccessibleInterval< T > proba, final double[] calibration, final double threshold, final boolean simplify, final double smoothingScale ) { return MaskUtils.fromThresholdWithROI( proba, @@ -190,6 +190,7 @@ public List< Spot > getSpots( final RandomAccessibleInterval< T > proba, final d calibration, threshold, simplify, + smoothingScale, numThreads, proba ); } diff --git a/src/test/java/fiji/plugin/trackmate/weka/WekaTestDrive.java b/src/test/java/fiji/plugin/trackmate/weka/WekaTestDrive.java index 22d6646..7df2b45 100644 --- a/src/test/java/fiji/plugin/trackmate/weka/WekaTestDrive.java +++ b/src/test/java/fiji/plugin/trackmate/weka/WekaTestDrive.java @@ -54,7 +54,6 @@ public static < T extends RealType< T > & NativeType< T > > void main( final Str final ImagePlus imp = IJ.openImage( targetImagePath ); imp.show(); - @SuppressWarnings( "unchecked" ) final ImgPlus< T > allChannels = TMUtils.rawWraps( imp ); final long targetChannel = 0; final long targetFrame = 0; @@ -94,7 +93,8 @@ public static < T extends RealType< T > & NativeType< T > > void main( final Str return; } - final List< Spot > spots0 = wekaRunner.getSpotsFromLastProbabilities( probaThreshold, simplify ); + final double smoothingScale = -1.; + final List< Spot > spots0 = wekaRunner.getSpotsFromLastProbabilities( probaThreshold, simplify, smoothingScale ); if ( spots0 == null ) { System.err.println( "Problem creating spots: " + wekaRunner.getErrorMessage() ); @@ -129,7 +129,7 @@ public static < T extends RealType< T > & NativeType< T > > void main( final Str final long start1 = System.currentTimeMillis(); final double probaThreshold2 = 0.8; - final List< Spot > spots1 = wekaRunner.getSpotsFromLastProbabilities( probaThreshold2, simplify ); + final List< Spot > spots1 = wekaRunner.getSpotsFromLastProbabilities( probaThreshold2, simplify, smoothingScale ); final long end1 = System.currentTimeMillis(); System.out.println( String.format( "Second run took %.2f seconds to run.", ( end1 - start1 ) / 1000. ) ); From 678b38725f4c29727265629c2614fd06ad7ae155 Mon Sep 17 00:00:00 2001 From: Jean-Yves Tinevez Date: Wed, 29 Nov 2023 18:58:43 +0100 Subject: [PATCH 07/13] Clean the test drives. --- .../trackmate/weka/LoadTrackMateWekaTestDrive.java | 6 +----- .../trackmate/weka/TrackMateWeka3DTestDrive.java | 12 +++--------- .../trackmate/weka/TrackMateWekaTestDrive.java | 10 ++-------- 3 files changed, 6 insertions(+), 22 deletions(-) diff --git a/src/test/java/fiji/plugin/trackmate/weka/LoadTrackMateWekaTestDrive.java b/src/test/java/fiji/plugin/trackmate/weka/LoadTrackMateWekaTestDrive.java index 9758b55..54a86e0 100644 --- a/src/test/java/fiji/plugin/trackmate/weka/LoadTrackMateWekaTestDrive.java +++ b/src/test/java/fiji/plugin/trackmate/weka/LoadTrackMateWekaTestDrive.java @@ -21,18 +21,14 @@ */ package fiji.plugin.trackmate.weka; -import javax.swing.UIManager; -import javax.swing.UnsupportedLookAndFeelException; - import fiji.plugin.trackmate.LoadTrackMatePlugIn; import ij.ImageJ; public class LoadTrackMateWekaTestDrive { - public static void main( final String[] args ) throws ClassNotFoundException, InstantiationException, IllegalAccessException, UnsupportedLookAndFeelException + public static void main( final String[] args ) { - UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); ImageJ.main( args ); final String path = "samples/crop-2tp.xml"; new LoadTrackMatePlugIn().run( path ); diff --git a/src/test/java/fiji/plugin/trackmate/weka/TrackMateWeka3DTestDrive.java b/src/test/java/fiji/plugin/trackmate/weka/TrackMateWeka3DTestDrive.java index ea5d71a..16b6090 100644 --- a/src/test/java/fiji/plugin/trackmate/weka/TrackMateWeka3DTestDrive.java +++ b/src/test/java/fiji/plugin/trackmate/weka/TrackMateWeka3DTestDrive.java @@ -21,11 +21,6 @@ */ package fiji.plugin.trackmate.weka; -import java.io.IOException; - -import javax.swing.UIManager; -import javax.swing.UnsupportedLookAndFeelException; - import fiji.plugin.trackmate.TrackMatePlugIn; import ij.IJ; import ij.ImageJ; @@ -33,12 +28,11 @@ public class TrackMateWeka3DTestDrive { - public static void main( final String[] args ) throws IOException, ClassNotFoundException, InstantiationException, IllegalAccessException, UnsupportedLookAndFeelException + public static void main( final String[] args ) { - UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); ImageJ.main( args ); -// final String path = "samples/merged.tif"; - final String path = "samples/mesh/CElegansMask3D.tif"; + final String path = "samples/merged.tif"; +// final String path = "samples/mesh/CElegansMask3D.tif"; IJ.openImage( path ).show(); new TrackMatePlugIn().run( null ); } diff --git a/src/test/java/fiji/plugin/trackmate/weka/TrackMateWekaTestDrive.java b/src/test/java/fiji/plugin/trackmate/weka/TrackMateWekaTestDrive.java index 2f5a597..34d889c 100644 --- a/src/test/java/fiji/plugin/trackmate/weka/TrackMateWekaTestDrive.java +++ b/src/test/java/fiji/plugin/trackmate/weka/TrackMateWekaTestDrive.java @@ -21,11 +21,6 @@ */ package fiji.plugin.trackmate.weka; -import java.io.IOException; - -import javax.swing.UIManager; -import javax.swing.UnsupportedLookAndFeelException; - import fiji.plugin.trackmate.TrackMatePlugIn; import ij.IJ; import ij.ImageJ; @@ -33,11 +28,10 @@ public class TrackMateWekaTestDrive { - public static void main( final String[] args ) throws IOException, ClassNotFoundException, InstantiationException, IllegalAccessException, UnsupportedLookAndFeelException + public static void main( final String[] args ) { - UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() ); ImageJ.main( args ); - final String path = "samples/crop-2tp.tif"; + final String path = "samples/MAX_Merged.tif"; IJ.openImage( path ).show(); new TrackMatePlugIn().run( null ); } From d686ce978005f95fc71e225cef60177eb323a9ea Mon Sep 17 00:00:00 2001 From: Jean-Yves Tinevez Date: Mon, 4 Dec 2023 17:16:08 +0100 Subject: [PATCH 08/13] Change factory priority to have consistent detector menu ordering. --- .../java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java b/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java index e970dbb..135f368 100644 --- a/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java +++ b/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java @@ -40,6 +40,7 @@ import javax.swing.ImageIcon; import org.jdom2.Element; +import org.scijava.Priority; import org.scijava.plugin.Plugin; import fiji.plugin.trackmate.Model; @@ -55,7 +56,7 @@ import net.imglib2.type.NativeType; import net.imglib2.type.numeric.RealType; -@Plugin( type = SpotDetectorFactory.class ) +@Plugin( type = SpotDetectorFactory.class, priority = Priority.LOW - 4.1 ) public class WekaDetectorFactory< T extends RealType< T > & NativeType< T > > implements SpotDetectorFactory< T > { From 0bf9da34858492da49806c5e4cf67f009d862140 Mon Sep 17 00:00:00 2001 From: Jean-Yves TINEVEZ Date: Wed, 1 May 2024 18:31:06 +0200 Subject: [PATCH 09/13] Remove duplicate license file. --- LICENSE | 674 -------------------------------------------------------- 1 file changed, 674 deletions(-) delete mode 100644 LICENSE diff --git a/LICENSE b/LICENSE deleted file mode 100644 index f288702..0000000 --- a/LICENSE +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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If not, see . - -Also add information on how to contact you by electronic and paper mail. - - If the program does terminal interaction, make it output a short -notice like this when it starts in an interactive mode: - - Copyright (C) - This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. - This is free software, and you are welcome to redistribute it - under certain conditions; type `show c' for details. - -The hypothetical commands `show w' and `show c' should show the appropriate -parts of the General Public License. Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". - - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -. - - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. From 0633a9a2bbfc6bd6f958cc504cec27cfb9745f9b Mon Sep 17 00:00:00 2001 From: Jean-Yves TINEVEZ Date: Wed, 1 May 2024 18:31:37 +0200 Subject: [PATCH 10/13] Add smoothing of spots. Same comment that for when we added it to the ilastik detector. --- .../weka/WekaDetectorConfigurationPanel.java | 30 +++++++++++++++++-- .../trackmate/weka/WekaDetectorFactory.java | 9 +++++- 2 files changed, 35 insertions(+), 4 deletions(-) diff --git a/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorConfigurationPanel.java b/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorConfigurationPanel.java index 2178dde..a772a32 100644 --- a/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorConfigurationPanel.java +++ b/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorConfigurationPanel.java @@ -22,6 +22,7 @@ package fiji.plugin.trackmate.weka; import static fiji.plugin.trackmate.detection.DetectorKeys.KEY_TARGET_CHANNEL; +import static fiji.plugin.trackmate.detection.ThresholdDetectorFactory.KEY_SMOOTHING_SCALE; import static fiji.plugin.trackmate.gui.Fonts.BIG_FONT; import static fiji.plugin.trackmate.gui.Fonts.FONT; import static fiji.plugin.trackmate.gui.Fonts.SMALL_FONT; @@ -64,6 +65,7 @@ import fiji.plugin.trackmate.Settings; import fiji.plugin.trackmate.gui.GuiUtils; import fiji.plugin.trackmate.gui.components.ConfigurationPanel; +import fiji.plugin.trackmate.gui.components.PanelSmoothContour; import fiji.plugin.trackmate.util.EverythingDisablerAndReenabler; import fiji.plugin.trackmate.util.FileChooser; import fiji.plugin.trackmate.util.FileChooser.DialogType; @@ -102,6 +104,8 @@ public class WekaDetectorConfigurationPanel extends ConfigurationPanel private final boolean is3D; + private final PanelSmoothContour smoothingPanel; + /** * Create the panel. */ @@ -258,6 +262,20 @@ public WekaDetectorConfigurationPanel( final Settings settings, final Model mode gbcScore.gridy = 6; add( ftfProbaThreshold, gbcScore ); + /* + * Smooth output. + */ + + smoothingPanel = new PanelSmoothContour( -1., model.getSpaceUnits() ); + final GridBagConstraints gbSmoothPanel = new GridBagConstraints(); + gbSmoothPanel.anchor = GridBagConstraints.NORTHWEST; + gbSmoothPanel.insets = new Insets( 5, 5, 5, 5 ); + gbSmoothPanel.gridwidth = 3; + gbSmoothPanel.gridx = 0; + gbSmoothPanel.gridy = 7; + gbSmoothPanel.fill = GridBagConstraints.HORIZONTAL; + this.add( smoothingPanel, gbSmoothPanel ); + /* * Refresh class names. */ @@ -269,7 +287,7 @@ public WekaDetectorConfigurationPanel( final Settings settings, final Model mode gbcBtnClassNames.anchor = GridBagConstraints.SOUTHWEST; gbcBtnClassNames.insets = new Insets( 5, 5, 5, 5 ); gbcBtnClassNames.gridx = 0; - gbcBtnClassNames.gridy = 7; + gbcBtnClassNames.gridy = 8; add( btnClassNames, gbcBtnClassNames ); /* @@ -283,7 +301,7 @@ public WekaDetectorConfigurationPanel( final Settings settings, final Model mode gbcBtnLastProba.anchor = GridBagConstraints.SOUTHEAST; gbcBtnLastProba.insets = new Insets( 5, 5, 5, 5 ); gbcBtnLastProba.gridx = 1; - gbcBtnLastProba.gridy = 7; + gbcBtnLastProba.gridy = 8; add( btnLastProba, gbcBtnLastProba ); /* @@ -295,7 +313,7 @@ public WekaDetectorConfigurationPanel( final Settings settings, final Model mode gbcBtnPreview.fill = GridBagConstraints.BOTH; gbcBtnPreview.insets = new Insets( 5, 5, 5, 5 ); gbcBtnPreview.gridx = 0; - gbcBtnPreview.gridy = 8; + gbcBtnPreview.gridy = 9; previewer = new WekaDetectionPreviewer<>( model, @@ -357,6 +375,9 @@ public Map< String, Object > getSettings() final double probaThreshold = ( ( Number ) ftfProbaThreshold.getValue() ).doubleValue(); settings.put( KEY_PROBA_THRESHOLD, probaThreshold ); + + final double scale = smoothingPanel.getScale(); + settings.put( KEY_SMOOTHING_SCALE, scale ); return settings; } @@ -370,6 +391,9 @@ public void setSettings( final Map< String, Object > settings ) cmbboxClassId.setSelectedIndex( ( Integer ) settings.get( KEY_CLASS_INDEX ) ); sliderChannel.setValue( ( Integer ) settings.get( KEY_TARGET_CHANNEL ) ); ftfProbaThreshold.setValue( settings.get( KEY_PROBA_THRESHOLD ) ); + final Object scaleObj = settings.get( KEY_SMOOTHING_SCALE ); + final double scale = scaleObj == null ? -1. : ( ( Number ) scaleObj ).doubleValue(); + smoothingPanel.setScale( scale ); } @Override diff --git a/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java b/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java index 135f368..16e6bc7 100644 --- a/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java +++ b/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorFactory.java @@ -30,6 +30,7 @@ import static fiji.plugin.trackmate.io.IOUtils.writeAttribute; import static fiji.plugin.trackmate.io.IOUtils.writeTargetChannel; import static fiji.plugin.trackmate.util.TMUtils.checkMapKeys; +import static fiji.plugin.trackmate.util.TMUtils.checkOptionalParameter; import static fiji.plugin.trackmate.util.TMUtils.checkParameter; import java.util.ArrayList; @@ -205,6 +206,7 @@ public boolean marshall( final Map< String, Object > settings, final Element ele ok = ok && writeAttribute( settings, element, KEY_CLASSIFIER_FILEPATH, String.class, errorHolder ); ok = ok && writeAttribute( settings, element, KEY_CLASS_INDEX, Integer.class, errorHolder ); ok = ok && writeAttribute( settings, element, KEY_PROBA_THRESHOLD, Double.class, errorHolder ); + ok = ok && writeAttribute( settings, element, KEY_SMOOTHING_SCALE, Double.class, errorHolder ); if ( !ok ) errorMessage = errorHolder.toString(); @@ -222,6 +224,7 @@ public boolean unmarshall( final Element element, final Map< String, Object > se ok = ok && readStringAttribute( element, settings, KEY_CLASSIFIER_FILEPATH, errorHolder ); ok = ok && readIntegerAttribute( element, settings, KEY_CLASS_INDEX, errorHolder ); ok = ok && readDoubleAttribute( element, settings, KEY_PROBA_THRESHOLD, errorHolder ); + ok = ok & readDoubleAttribute( element, settings, KEY_SMOOTHING_SCALE, errorHolder ); if ( !ok ) { @@ -245,6 +248,7 @@ public Map< String, Object > getDefaultSettings() settings.put( KEY_CLASS_INDEX, DEFAULT_CLASS_INDEX ); settings.put( KEY_PROBA_THRESHOLD, DEFAULT_PROBA_THRESHOLD ); settings.put( KEY_CLASSIFIER_FILEPATH, null ); + settings.put( KEY_SMOOTHING_SCALE, -1. ); return settings; } @@ -257,12 +261,15 @@ public boolean checkSettings( final Map< String, Object > settings ) ok = ok & checkParameter( settings, KEY_CLASS_INDEX, Integer.class, errorHolder ); ok = ok & checkParameter( settings, KEY_PROBA_THRESHOLD, Double.class, errorHolder ); ok = ok & checkParameter( settings, KEY_CLASSIFIER_FILEPATH, String.class, errorHolder ); + ok = ok & checkOptionalParameter( settings, KEY_SMOOTHING_SCALE, Double.class, errorHolder ); final List< String > mandatoryKeys = new ArrayList<>(); mandatoryKeys.add( KEY_TARGET_CHANNEL ); mandatoryKeys.add( KEY_CLASS_INDEX ); mandatoryKeys.add( KEY_PROBA_THRESHOLD ); mandatoryKeys.add( KEY_CLASSIFIER_FILEPATH ); - ok = ok & checkMapKeys( settings, mandatoryKeys, null, errorHolder ); + final List< String > optionalKeys = new ArrayList<>(); + optionalKeys.add( KEY_SMOOTHING_SCALE ); + ok = ok & checkMapKeys( settings, mandatoryKeys, optionalKeys, errorHolder ); if ( !ok ) errorMessage = errorHolder.toString(); From 079e20223fd46c5e6a9ec7200c408029d42a8ddb Mon Sep 17 00:00:00 2001 From: Jean-Yves TINEVEZ Date: Wed, 1 May 2024 18:35:15 +0200 Subject: [PATCH 11/13] Use the proba threshold widget. --- .../weka/WekaDetectorConfigurationPanel.java | 39 +++++++------------ 1 file changed, 14 insertions(+), 25 deletions(-) diff --git a/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorConfigurationPanel.java b/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorConfigurationPanel.java index a772a32..c600d5d 100644 --- a/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorConfigurationPanel.java +++ b/src/main/java/fiji/plugin/trackmate/weka/WekaDetectorConfigurationPanel.java @@ -31,15 +31,12 @@ import static fiji.plugin.trackmate.weka.WekaDetectorFactory.KEY_CLASS_INDEX; import static fiji.plugin.trackmate.weka.WekaDetectorFactory.KEY_PROBA_THRESHOLD; -import java.awt.Dimension; import java.awt.GridBagConstraints; import java.awt.GridBagLayout; import java.awt.Insets; import java.beans.PropertyChangeListener; import java.io.File; import java.net.URL; -import java.text.DecimalFormat; -import java.text.NumberFormat; import java.util.Arrays; import java.util.HashMap; import java.util.List; @@ -50,7 +47,6 @@ import javax.swing.ImageIcon; import javax.swing.JButton; import javax.swing.JComboBox; -import javax.swing.JFormattedTextField; import javax.swing.JLabel; import javax.swing.JSlider; import javax.swing.JTextField; @@ -65,6 +61,7 @@ import fiji.plugin.trackmate.Settings; import fiji.plugin.trackmate.gui.GuiUtils; import fiji.plugin.trackmate.gui.components.ConfigurationPanel; +import fiji.plugin.trackmate.gui.components.PanelProbaThreshold; import fiji.plugin.trackmate.gui.components.PanelSmoothContour; import fiji.plugin.trackmate.util.EverythingDisablerAndReenabler; import fiji.plugin.trackmate.util.FileChooser; @@ -80,8 +77,6 @@ public class WekaDetectorConfigurationPanel extends ConfigurationPanel private static final long serialVersionUID = 1L; - private static final NumberFormat THRESHOLD_FORMAT = new DecimalFormat( "#.##" ); - protected static final ImageIcon ICON = new ImageIcon( getResource( "images/TrackMateWeka-logo-100px.png" ) ); private static final String TITLE = WekaDetectorFactory.NAME; @@ -96,8 +91,6 @@ public class WekaDetectorConfigurationPanel extends ConfigurationPanel private final JButton btnBrowse; - private final JFormattedTextField ftfProbaThreshold; - protected final PrefService prefService; private final WekaDetectionPreviewer< ? > previewer; @@ -106,6 +99,8 @@ public class WekaDetectorConfigurationPanel extends ConfigurationPanel private final PanelSmoothContour smoothingPanel; + private final PanelProbaThreshold probaThresholdPanel; + /** * Create the panel. */ @@ -242,25 +237,15 @@ public WekaDetectorConfigurationPanel( final Settings settings, final Model mode * Proba threshold. */ - final JLabel lblScoreTreshold = new JLabel( "Threshold on probability:" ); - lblScoreTreshold.setFont( SMALL_FONT ); - final GridBagConstraints gbcLblScoreTreshold = new GridBagConstraints(); - gbcLblScoreTreshold.anchor = GridBagConstraints.EAST; - gbcLblScoreTreshold.insets = new Insets( 5, 5, 5, 5 ); - gbcLblScoreTreshold.gridx = 0; - gbcLblScoreTreshold.gridy = 6; - add( lblScoreTreshold, gbcLblScoreTreshold ); - - ftfProbaThreshold = new JFormattedTextField( THRESHOLD_FORMAT ); - ftfProbaThreshold.setFont( SMALL_FONT ); - ftfProbaThreshold.setMinimumSize( new Dimension( 60, 20 ) ); - ftfProbaThreshold.setHorizontalAlignment( SwingConstants.CENTER ); + probaThresholdPanel = new PanelProbaThreshold( 0.5 ); final GridBagConstraints gbcScore = new GridBagConstraints(); gbcScore.fill = GridBagConstraints.HORIZONTAL; + gbcScore.anchor = GridBagConstraints.NORTHWEST; gbcScore.insets = new Insets( 5, 5, 5, 5 ); - gbcScore.gridx = 1; + gbcScore.gridx = 0; gbcScore.gridy = 6; - add( ftfProbaThreshold, gbcScore ); + gbcScore.gridwidth = 3; + add( probaThresholdPanel, gbcScore ); /* * Smooth output. @@ -373,7 +358,7 @@ public Map< String, Object > getSettings() final int classID = cmbboxClassId.getSelectedIndex(); settings.put( KEY_CLASS_INDEX, classID ); - final double probaThreshold = ( ( Number ) ftfProbaThreshold.getValue() ).doubleValue(); + final double probaThreshold = probaThresholdPanel.getThreshold(); settings.put( KEY_PROBA_THRESHOLD, probaThreshold ); final double scale = smoothingPanel.getScale(); @@ -390,7 +375,11 @@ public void setSettings( final Map< String, Object > settings ) modelFileTextField.setText( filePath ); cmbboxClassId.setSelectedIndex( ( Integer ) settings.get( KEY_CLASS_INDEX ) ); sliderChannel.setValue( ( Integer ) settings.get( KEY_TARGET_CHANNEL ) ); - ftfProbaThreshold.setValue( settings.get( KEY_PROBA_THRESHOLD ) ); + + final Object thresholdObj = settings.get( KEY_PROBA_THRESHOLD ); + final double threshold = thresholdObj == null ? -1. : ( ( Number ) thresholdObj ).doubleValue(); + probaThresholdPanel.setThreshold( threshold ); + final Object scaleObj = settings.get( KEY_SMOOTHING_SCALE ); final double scale = scaleObj == null ? -1. : ( ( Number ) scaleObj ).doubleValue(); smoothingPanel.setScale( scale ); From 6e9e6bef044855244a90337fe8b27215e6c7800d Mon Sep 17 00:00:00 2001 From: Jean-Yves TINEVEZ Date: Wed, 1 May 2024 18:36:16 +0200 Subject: [PATCH 12/13] Tweak test drive. --- .../java/fiji/plugin/trackmate/weka/TrackMateWekaTestDrive.java | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/test/java/fiji/plugin/trackmate/weka/TrackMateWekaTestDrive.java b/src/test/java/fiji/plugin/trackmate/weka/TrackMateWekaTestDrive.java index 34d889c..fd6891c 100644 --- a/src/test/java/fiji/plugin/trackmate/weka/TrackMateWekaTestDrive.java +++ b/src/test/java/fiji/plugin/trackmate/weka/TrackMateWekaTestDrive.java @@ -22,6 +22,7 @@ package fiji.plugin.trackmate.weka; import fiji.plugin.trackmate.TrackMatePlugIn; +import fiji.plugin.trackmate.gui.GuiUtils; import ij.IJ; import ij.ImageJ; @@ -30,6 +31,7 @@ public class TrackMateWekaTestDrive public static void main( final String[] args ) { + GuiUtils.setSystemLookAndFeel(); ImageJ.main( args ); final String path = "samples/MAX_Merged.tif"; IJ.openImage( path ).show(); From 3b928e90e462458747931cc84e32dea83be6973f Mon Sep 17 00:00:00 2001 From: Jean-Yves TINEVEZ Date: Wed, 1 May 2024 18:37:11 +0200 Subject: [PATCH 13/13] Fix minor Eclipse warning. --- src/main/java/fiji/plugin/trackmate/weka/WekaRunner.java | 1 - 1 file changed, 1 deletion(-) diff --git a/src/main/java/fiji/plugin/trackmate/weka/WekaRunner.java b/src/main/java/fiji/plugin/trackmate/weka/WekaRunner.java index 1a40dec..4a3d7cb 100644 --- a/src/main/java/fiji/plugin/trackmate/weka/WekaRunner.java +++ b/src/main/java/fiji/plugin/trackmate/weka/WekaRunner.java @@ -131,7 +131,6 @@ public RandomAccessibleInterval< T > computeProbabilities( final ImagePlus probas = segmentation.applyClassifier( vimp, numThreads, true ); // Convert to Img and extract desired class. - @SuppressWarnings( "unchecked" ) final ImgPlus< T > probaImp = TMUtils.rawWraps( probas ); final ImgPlus< T > classProba = TMUtils.hyperSlice( probaImp, classId, 0 );