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qupath / qupath-weka-extension

Extension to enable Weka within QuPath - **QuPath v0.1.2 only**
GNU General Public License v3.0
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Exporting training data for Weka does not work in QuPath 0.2.0 m8 #3

Closed bpuladi closed 4 years ago

bpuladi commented 4 years ago

Hi Pete, unfortunately exporting training data for Weka does not work in QuPath 0.2.0 m8. I added the log. Best greetings BP

INFO: Refreshing extensions in E:\Software\QuPath Extensions\extensions
INFO: Added extension: E:\Software\QuPath Extensions\extensions\qupath-weka-extension.jar
INFO: Bio-Formats version 6.3.0
INFO: Loaded extension Bio-Formats server options (Bio-Formats 6.3.0) (15 ms)
INFO: Loaded extension Experimental commands (29 ms)
INFO: Loaded extension ImageJ extension (40 ms)
INFO: Loaded extension JPen extension (20 ms)
INFO: Loaded extension OpenCV extensions (3 ms)
INFO: Loaded extension Rich script editor extension (283 ms)
INFO: Loaded extension Weka classifier extension (5 ms)
INFO: OpenSlide version 3.4.1
INFO: Selected style: null
INFO: Performing update check...
INFO: Starting QuPath with parameters: []
WARN: Temp memoization directory created at C:\Users\Behrus\AppData\Local\Temp\qupath-memo-8584360664841369225
WARN: If you want to avoid this warning, either disable Bio-Formats memoization in the preferences or specify a directory to use
INFO: Reading data from HNSCC-15-10967-22C3 - 2019-03-22 20.25.34.qpdata...
INFO: Image data set to ImageData: Brightfield (H-DAB), HNSCC-15-10967-22C3 - 2019-03-22 20.25.34.ndpi
INFO: 7 nuclei detected (processing time: 0.31 seconds)
INFO: 33 nuclei detected (processing time: 1.64 seconds)
INFO: 378 nuclei detected (processing time: 3.98 seconds)
INFO: 560 nuclei detected (processing time: 4.83 seconds)
INFO: 2731 nuclei detected (processing time: 10.33 seconds)
INFO: 1285 nuclei detected (processing time: 11.71 seconds)
INFO: 3798 nuclei detected (processing time: 12.46 seconds)
INFO: 2315 nuclei detected (processing time: 13.59 seconds)
INFO: 1029 nuclei detected (processing time: 3.33 seconds)
INFO: 1856 nuclei detected (processing time: 6.20 seconds)
INFO: 4285 nuclei detected (processing time: 9.36 seconds)
INFO: 799 nuclei detected (processing time: 18.53 seconds)
INFO: 3063 nuclei detected (processing time: 17.16 seconds)
INFO: 2613 nuclei detected (processing time: 7.71 seconds)
INFO: 3075 nuclei detected (processing time: 6.90 seconds)
INFO: 6664 nuclei detected (processing time: 21.12 seconds)
INFO: 8475 nuclei detected (processing time: 21.29 seconds)
INFO: 6520 nuclei detected (processing time: 21.40 seconds)
INFO: 4871 nuclei detected (processing time: 21.50 seconds)
INFO: 787 nuclei detected (processing time: 2.87 seconds)
INFO: 2874 nuclei detected (processing time: 22.67 seconds)
INFO: 1196 nuclei detected (processing time: 4.10 seconds)
INFO: 999 nuclei detected (processing time: 4.15 seconds)
INFO: 2122 nuclei detected (processing time: 11.42 seconds)
INFO: 3478 nuclei detected (processing time: 13.50 seconds)
INFO: 3053 nuclei detected (processing time: 9.08 seconds)
INFO: 455 nuclei detected (processing time: 1.42 seconds)
INFO: 3037 nuclei detected (processing time: 11.40 seconds)
INFO: 1021 nuclei detected (processing time: 6.65 seconds)
INFO: 765 nuclei detected (processing time: 2.14 seconds)
INFO: 7661 nuclei detected (processing time: 21.72 seconds)
INFO: 2232 nuclei detected (processing time: 10.93 seconds)
INFO: 25 nuclei detected (processing time: 0.14 seconds)
INFO: 8200 nuclei detected (processing time: 25.48 seconds)
INFO: 5932 nuclei detected (processing time: 22.14 seconds)
INFO: 1199 nuclei detected (processing time: 4.29 seconds)
INFO: 7574 nuclei detected (processing time: 23.62 seconds)
INFO: 8523 nuclei detected (processing time: 23.79 seconds)
INFO: 151 nuclei detected (processing time: 0.39 seconds)
INFO: 1708 nuclei detected (processing time: 4.71 seconds)
INFO: 6683 nuclei detected (processing time: 23.20 seconds)
INFO: 6724 nuclei detected (processing time: 22.10 seconds)
INFO: 86 nuclei detected (processing time: 0.36 seconds)
INFO: 786 nuclei detected (processing time: 1.71 seconds)
INFO: 6054 nuclei detected (processing time: 23.73 seconds)
INFO: 1134 nuclei detected (processing time: 3.51 seconds)
INFO: 6760 nuclei detected (processing time: 17.28 seconds)
INFO: 3258 nuclei detected (processing time: 8.00 seconds)
INFO: 3372 nuclei detected (processing time: 17.89 seconds)
INFO: 112 nuclei detected (processing time: 0.23 seconds)
INFO: 3163 nuclei detected (processing time: 11.04 seconds)
INFO: 2229 nuclei detected (processing time: 9.31 seconds)
INFO: 6886 nuclei detected (processing time: 24.57 seconds)
INFO: 6 nuclei detected (processing time: 0.09 seconds)
INFO: 35 nuclei detected (processing time: 0.26 seconds)
INFO: 655 nuclei detected (processing time: 3.45 seconds)
INFO: 4953 nuclei detected (processing time: 11.95 seconds)
INFO: 3346 nuclei detected (processing time: 17.98 seconds)
INFO: 6080 nuclei detected (processing time: 20.39 seconds)
INFO: 5987 nuclei detected (processing time: 14.60 seconds)
INFO: 4548 nuclei detected (processing time: 16.40 seconds)
INFO: 1773 nuclei detected (processing time: 8.16 seconds)
INFO: 5016 nuclei detected (processing time: 18.91 seconds)
INFO: 725 nuclei detected (processing time: 8.04 seconds)
INFO: 6331 nuclei detected (processing time: 22.82 seconds)
INFO: 7896 nuclei detected (processing time: 22.42 seconds)
INFO: 4952 nuclei detected (processing time: 18.46 seconds)
INFO: 2673 nuclei detected (processing time: 7.98 seconds)
INFO: 3580 nuclei detected (processing time: 18.35 seconds)
INFO: 158 nuclei detected (processing time: 0.37 seconds)
INFO: 2602 nuclei detected (processing time: 13.14 seconds)
INFO: 5210 nuclei detected (processing time: 24.71 seconds)
INFO: 6349 nuclei detected (processing time: 14.60 seconds)
INFO: 127 nuclei detected (processing time: 0.50 seconds)
INFO: 21 nuclei detected (processing time: 1.10 seconds)
INFO: 4090 nuclei detected (processing time: 14.39 seconds)
INFO: 4894 nuclei detected (processing time: 17.26 seconds)
INFO: 6821 nuclei detected (processing time: 25.15 seconds)
INFO: 7231 nuclei detected (processing time: 19.81 seconds)
INFO: 8615 nuclei detected (processing time: 22.73 seconds)
INFO: 2505 nuclei detected (processing time: 12.06 seconds)
INFO: 769 nuclei detected (processing time: 1.72 seconds)
INFO: 90 nuclei detected (processing time: 15.24 seconds)
INFO: 190 nuclei detected (processing time: 1.39 seconds)
INFO: 4598 nuclei detected (processing time: 18.62 seconds)
INFO: 3276 nuclei detected (processing time: 15.00 seconds)
INFO: 5854 nuclei detected (processing time: 24.22 seconds)
INFO: 10094 nuclei detected (processing time: 26.49 seconds)
INFO: 5367 nuclei detected (processing time: 14.69 seconds)
INFO: 2647 nuclei detected (processing time: 6.14 seconds)
INFO: 70 nuclei detected (processing time: 0.36 seconds)
INFO: 1387 nuclei detected (processing time: 10.89 seconds)
INFO: 2238 nuclei detected (processing time: 21.12 seconds)
INFO: 8467 nuclei detected (processing time: 25.03 seconds)
INFO: 4375 nuclei detected (processing time: 13.30 seconds)
INFO: 4205 nuclei detected (processing time: 15.12 seconds)
INFO: 6411 nuclei detected (processing time: 24.45 seconds)
INFO: 10243 nuclei detected (processing time: 24.06 seconds)
INFO: 2110 nuclei detected (processing time: 16.15 seconds)
INFO: 7780 nuclei detected (processing time: 20.33 seconds)
INFO: 8041 nuclei detected (processing time: 25.64 seconds)
INFO: 2587 nuclei detected (processing time: 21.13 seconds)
INFO: 5750 nuclei detected (processing time: 11.94 seconds)
INFO: 9120 nuclei detected (processing time: 21.72 seconds)
INFO: 1347 nuclei detected (processing time: 8.68 seconds)
INFO: 3610 nuclei detected (processing time: 7.50 seconds)
INFO: 8035 nuclei detected (processing time: 23.13 seconds)
INFO: 5588 nuclei detected (processing time: 14.78 seconds)
INFO: 9286 nuclei detected (processing time: 23.52 seconds)
INFO: 9378 nuclei detected (processing time: 22.63 seconds)
INFO: 2080 nuclei detected (processing time: 14.27 seconds)
INFO: 3451 nuclei detected (processing time: 22.69 seconds)
INFO: 2486 nuclei detected (processing time: 19.87 seconds)
INFO: 8179 nuclei detected (processing time: 26.72 seconds)
INFO: 5830 nuclei detected (processing time: 22.74 seconds)
INFO: 6680 nuclei detected (processing time: 18.08 seconds)
INFO: 8078 nuclei detected (processing time: 27.38 seconds)
INFO: 2981 nuclei detected (processing time: 10.32 seconds)
INFO: 5012 nuclei detected (processing time: 31.02 seconds)
INFO: 4109 nuclei detected (processing time: 14.61 seconds)
INFO: 3627 nuclei detected (processing time: 11.43 seconds)
INFO: 11166 nuclei detected (processing time: 27.54 seconds)
INFO: 2702 nuclei detected (processing time: 20.36 seconds)
INFO: 7857 nuclei detected (processing time: 18.56 seconds)
INFO: 2953 nuclei detected (processing time: 14.27 seconds)
INFO: 3542 nuclei detected (processing time: 24.25 seconds)
INFO: 10093 nuclei detected (processing time: 30.85 seconds)
INFO: 4338 nuclei detected (processing time: 23.17 seconds)
INFO: 5414 nuclei detected (processing time: 23.72 seconds)
INFO: 10983 nuclei detected (processing time: 28.12 seconds)
INFO: 428 nuclei detected (processing time: 1.68 seconds)
INFO: 9764 nuclei detected (processing time: 24.85 seconds)
INFO: 998 nuclei detected (processing time: 2.92 seconds)
INFO: 6952 nuclei detected (processing time: 22.74 seconds)
INFO: 3638 nuclei detected (processing time: 6.32 seconds)
INFO: 3353 nuclei detected (processing time: 9.83 seconds)
INFO: 8855 nuclei detected (processing time: 20.26 seconds)
INFO: 9433 nuclei detected (processing time: 23.00 seconds)
INFO: 10327 nuclei detected (processing time: 25.79 seconds)
INFO: 2147 nuclei detected (processing time: 19.90 seconds)
INFO: 94 nuclei detected (processing time: 0.50 seconds)
INFO: 11345 nuclei detected (processing time: 22.32 seconds)
INFO: 6500 nuclei detected (processing time: 17.90 seconds)
INFO: 9647 nuclei detected (processing time: 27.01 seconds)
INFO: 8607 nuclei detected (processing time: 28.18 seconds)
INFO: 2423 nuclei detected (processing time: 8.01 seconds)
INFO: 92 nuclei detected (processing time: 0.30 seconds)
INFO: 3178 nuclei detected (processing time: 8.50 seconds)
INFO: 9523 nuclei detected (processing time: 23.09 seconds)
INFO: 223 nuclei detected (processing time: 2.20 seconds)
INFO: 4621 nuclei detected (processing time: 10.93 seconds)
INFO: 10055 nuclei detected (processing time: 24.44 seconds)
INFO: 5244 nuclei detected (processing time: 11.59 seconds)
INFO: 10356 nuclei detected (processing time: 24.05 seconds)
INFO: 222 nuclei detected (processing time: 0.55 seconds)
INFO: 988 nuclei detected (processing time: 8.50 seconds)
INFO: 10484 nuclei detected (processing time: 20.85 seconds)
INFO: 10042 nuclei detected (processing time: 21.20 seconds)
INFO: 6333 nuclei detected (processing time: 22.01 seconds)
INFO: 5905 nuclei detected (processing time: 15.54 seconds)
INFO: 785 nuclei detected (processing time: 3.70 seconds)
INFO: 187 nuclei detected (processing time: 0.88 seconds)
INFO: 264 nuclei detected (processing time: 0.63 seconds)
INFO: 8487 nuclei detected (processing time: 18.02 seconds)
INFO: 854 nuclei detected (processing time: 2.17 seconds)
INFO: 3119 nuclei detected (processing time: 12.41 seconds)
INFO: 892 nuclei detected (processing time: 7.95 seconds)
INFO: 1538 nuclei detected (processing time: 2.97 seconds)
INFO: 11020 nuclei detected (processing time: 20.86 seconds)
INFO: 9768 nuclei detected (processing time: 19.61 seconds)
INFO: 5308 nuclei detected (processing time: 20.55 seconds)
INFO: 9568 nuclei detected (processing time: 23.73 seconds)
INFO: 8557 nuclei detected (processing time: 25.66 seconds)
INFO: 11507 nuclei detected (processing time: 25.33 seconds)
INFO: 11464 nuclei detected (processing time: 21.85 seconds)
INFO: 9625 nuclei detected (processing time: 23.57 seconds)
INFO: 6937 nuclei detected (processing time: 12.79 seconds)
INFO: 6437 nuclei detected (processing time: 13.23 seconds)
INFO: 6663 nuclei detected (processing time: 14.72 seconds)
INFO: 10782 nuclei detected (processing time: 14.96 seconds)
INFO: Processing complete in 225.57 seconds
INFO: Completed!
INFO: 
qupath.imagej.detect.cells.WatershedCellMembraneDetection  {"detectionImageBrightfield": "Hematoxylin",  "requestedPixelSizeMicrons": 0.5,  "backgroundRadiusMicrons": 8.0,  "medianRadiusMicrons": 0.0,  "sigmaMicrons": 1.5,  "minAreaMicrons": 10.0,  "maxAreaMicrons": 1000.0,  "threshold": 0.1,  "maxBackground": 0.5,  "watershedPostProcess": true,  "excludeDAB": true,  "cellExpansionMicrons": 25.0,  "limitExpansionByNucleusSize": false,  "includeNuclei": true,  "smoothBoundaries": false,  "makeMeasurements": true}
INFO: Writing object hierarchy with 667611 object(s)...
INFO: Image data written in 10.31 seconds
WARN: Smoothing using annotations
INFO: Processing complete in 13.52 seconds
INFO: Completed!
INFO: 
qupath.lib.plugins.objects.SmoothFeaturesPlugin  {"fwhmMicrons": 25.0,  "smoothWithinClasses": false,  "useLegacyNames": false}
INFO: Training size: org.bytedeco.opencv.opencv_core.Size[address=0x1e4bdfbabc0,position=0,limit=1,capacity=1,deallocator=org.bytedeco.javacpp.Pointer$NativeDeallocator[ownerAddress=0x1e4bdfbabc0,deallocatorAddress=0x7ffe7b695770]]
INFO: Responses size: org.bytedeco.opencv.opencv_core.Size[address=0x1e4bdfba940,position=0,limit=1,capacity=1,deallocator=org.bytedeco.javacpp.Pointer$NativeDeallocator[ownerAddress=0x1e4bdfba940,deallocatorAddress=0x7ffe7b695770]]
INFO: RTrees classifier termination criteria: org.bytedeco.opencv.opencv_core.TermCriteria[address=0x1e503b7c890,position=0,limit=1,capacity=1,deallocator=org.bytedeco.javacpp.Pointer$NativeDeallocator[ownerAddress=0x1e503b7c890,deallocatorAddress=0x7ffe7b695930]]
INFO: Classifier trained with 12897 samples
INFO: Reading classifier qupath.opencv.classify.RTreesClassifier@47c24c4c complete!
INFO: Classification time: 5.54 seconds
INFO: Classification time: 5.43 seconds
INFO: Writing object hierarchy with 667612 object(s)...
INFO: Image data written in 12.39 seconds
INFO: 1306 nuclei detected (processing time: 21.04 seconds)
INFO: Processing complete in 22.22 seconds
INFO: Completed!
INFO: 
qupath.imagej.detect.cells.WatershedCellMembraneDetection  {"detectionImageBrightfield": "Hematoxylin",  "requestedPixelSizeMicrons": 0.5,  "backgroundRadiusMicrons": 8.0,  "medianRadiusMicrons": 0.0,  "sigmaMicrons": 1.5,  "minAreaMicrons": 10.0,  "maxAreaMicrons": 1000.0,  "threshold": 0.1,  "maxBackground": 0.25,  "watershedPostProcess": true,  "excludeDAB": true,  "cellExpansionMicrons": 25.0,  "limitExpansionByNucleusSize": false,  "includeNuclei": true,  "smoothBoundaries": false,  "makeMeasurements": true}
INFO: Immune cells: 911
INFO: Stroma: 1306
INFO: Tumor: 3346
INFO: 5563 objects available for classifier training from 1 images
INFO: Cell: DAB OD max Quartile 1: 0.1877
INFO: Cell: DAB OD max Median: 0.3146
INFO: Cell: DAB OD max Quartile 3: 1.0504
INFO: Cell: DAB OD max Mean: 0.6354
INFO: Cell: DAB OD max Std.Dev.: 0.5982
INFO: Cell: DAB OD mean Quartile 1: 0.0653
INFO: Cell: DAB OD mean Median: 0.0984
INFO: Cell: DAB OD mean Quartile 3: 0.3279
INFO: Cell: DAB OD mean Mean: 0.2262
INFO: Cell: DAB OD mean Std.Dev.: 0.2480
INFO: Feature selection: Classifier set to train using all 75 available features
INFO: Immune cells: 911
INFO: Stroma: 1306
INFO: Tumor: 3346
INFO: 5563 objects available for classifier training from 1 images
INFO: Training size: org.bytedeco.opencv.opencv_core.Size[address=0x1e4b81a8040,position=0,limit=1,capacity=1,deallocator=org.bytedeco.javacpp.Pointer$NativeDeallocator[ownerAddress=0x1e4b81a8040,deallocatorAddress=0x7ffe7b695770]]
INFO: Responses size: org.bytedeco.opencv.opencv_core.Size[address=0x1e4b81a7f30,position=0,limit=1,capacity=1,deallocator=org.bytedeco.javacpp.Pointer$NativeDeallocator[ownerAddress=0x1e4b81a7f30,deallocatorAddress=0x7ffe7b695770]]
INFO: RTrees classifier termination criteria: org.bytedeco.opencv.opencv_core.TermCriteria[address=0x1e514e34960,position=0,limit=1,capacity=1,deallocator=org.bytedeco.javacpp.Pointer$NativeDeallocator[ownerAddress=0x1e514e34960,deallocatorAddress=0x7ffe7b695930]]
INFO: Classifier trained with 5563 samples
INFO: Classifier training time: 0.80 seconds
INFO: Classification time: 2.68 seconds
INFO: Percentage of correctly classified objects in TRAINING set: 11.16% (n=5563)
WARN: It is *strongly* advised not to report accuracies based on testing using the training set!
INFO: Number of unclassified objects in the test set: 1306 (23.48%)
INFO: Confusion matrix
                Immune cells          Stroma           Tumor
Immune cells             621               0             290
      Stroma               0               0               0
       Tumor            3346               0               0

INFO: Number of reclassified objects: 495353 of 668916
WARN: Smoothing using annotations
INFO: Processing complete in 0.04 seconds
INFO: Completed!
INFO: 
qupath.lib.plugins.objects.SmoothFeaturesPlugin  {"fwhmMicrons": 25.0,  "smoothWithinClasses": false,  "useLegacyNames": false}
INFO: Immune cells: 911
INFO: Stroma: 1306
INFO: Tumor: 3346
INFO: 5563 objects available for classifier training from 1 images
INFO: Cell: DAB OD max Quartile 1: 0.1877
INFO: Cell: DAB OD max Median: 0.3146
INFO: Cell: DAB OD max Quartile 3: 1.0504
INFO: Cell: DAB OD max Mean: 0.6354
INFO: Cell: DAB OD max Std.Dev.: 0.5982
INFO: Cell: DAB OD mean Quartile 1: 0.0653
INFO: Cell: DAB OD mean Median: 0.0984
INFO: Cell: DAB OD mean Quartile 3: 0.3279
INFO: Cell: DAB OD mean Mean: 0.2262
INFO: Cell: DAB OD mean Std.Dev.: 0.2480
INFO: Feature selection: Classifier set to train using all 75 available features
INFO: Immune cells: 911
INFO: Stroma: 1306
INFO: Tumor: 3346
INFO: 5563 objects available for classifier training from 1 images
INFO: Training size: org.bytedeco.opencv.opencv_core.Size[address=0x1e4b012fb00,position=0,limit=1,capacity=1,deallocator=org.bytedeco.javacpp.Pointer$NativeDeallocator[ownerAddress=0x1e4b012fb00,deallocatorAddress=0x7ffe7b695770]]
INFO: Responses size: org.bytedeco.opencv.opencv_core.Size[address=0x1e4b012fc50,position=0,limit=1,capacity=1,deallocator=org.bytedeco.javacpp.Pointer$NativeDeallocator[ownerAddress=0x1e4b012fc50,deallocatorAddress=0x7ffe7b695770]]
INFO: RTrees classifier termination criteria: org.bytedeco.opencv.opencv_core.TermCriteria[address=0x1e4be57fd10,position=0,limit=1,capacity=1,deallocator=org.bytedeco.javacpp.Pointer$NativeDeallocator[ownerAddress=0x1e4be57fd10,deallocatorAddress=0x7ffe7b695930]]
INFO: Classifier trained with 5563 samples
INFO: Classifier training time: 0.82 seconds
INFO: Classification time: 2.28 seconds
INFO: Percentage of correctly classified objects in TRAINING set: 99.98% (n=5563)
WARN: It is *strongly* advised not to report accuracies based on testing using the training set!
INFO: Confusion matrix
                Immune cells          Stroma           Tumor
Immune cells             911               0               0
      Stroma               0            1306               0
       Tumor               0               1            3345

INFO: Number of reclassified objects: 154274 of 668916
INFO: Writing classifier qupath.opencv.classify.RTreesClassifier@5374711 complete!
INFO: Immune cells: 911
INFO: Stroma: 1306
INFO: Tumor: 3346
INFO: 5563 objects available for classifier training from 1 images
INFO: Cell: DAB OD max Quartile 1: 0.1877
INFO: Cell: DAB OD max Median: 0.3146
INFO: Cell: DAB OD max Quartile 3: 1.0504
INFO: Cell: DAB OD max Mean: 0.6354
INFO: Cell: DAB OD max Std.Dev.: 0.5982
INFO: Cell: DAB OD mean Quartile 1: 0.0653
INFO: Cell: DAB OD mean Median: 0.0984
INFO: Cell: DAB OD mean Quartile 3: 0.3279
INFO: Cell: DAB OD mean Mean: 0.2262
INFO: Cell: DAB OD mean Std.Dev.: 0.2480
INFO: Feature selection: Classifier set to train using all 75 available features
INFO: Immune cells: 911
INFO: Stroma: 1306
INFO: Tumor: 3346
INFO: 5563 objects available for classifier training from 1 images
INFO: Classifier training time: 1.24 seconds
INFO: Classification time: 3.93 seconds
INFO: Percentage of correctly classified objects in TRAINING set: 100.00% (n=5563)
WARN: It is *strongly* advised not to report accuracies based on testing using the training set!
INFO: Confusion matrix
                Immune cells          Stroma           Tumor
Immune cells             911               0               0
      Stroma               0            1306               0
       Tumor               0               0            3346

INFO: Number of reclassified objects: 26156 of 668916
ERROR: QuPath exception: 'qupath.lib.gui.helpers.dialogs.DialogHelper qupath.lib.gui.QuPathGUI.getDialogHelper()'
    at qupath.extensions.weka.WekaClassifierCommand.saveWekaData(WekaClassifierCommand.java:192)
    at qupath.extensions.weka.WekaClassifierCommand.lambda$run$1(WekaClassifierCommand.java:137)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.Node.fireEvent(Node.java:8890)
    at javafx.scene.control.Button.fire(Button.java:203)
    at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:206)
    at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274)
    at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3862)
    at javafx.scene.Scene.processMouseEvent(Scene.java:1849)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2590)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299)
    at java.base/java.security.AccessController.doPrivileged(Unknown Source)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447)
    at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446)
    at com.sun.glass.ui.View.handleMouseEvent(View.java:556)
    at com.sun.glass.ui.View.notifyMouse(View.java:942)
    at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
    at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174)
    at java.base/java.lang.Thread.run(Unknown Source)
ERROR: QuPath exception: 'qupath.lib.gui.helpers.dialogs.DialogHelper qupath.lib.gui.QuPathGUI.getDialogHelper()'
    at qupath.extensions.weka.WekaClassifierCommand.saveWekaData(WekaClassifierCommand.java:192)
    at qupath.extensions.weka.WekaClassifierCommand.lambda$run$1(WekaClassifierCommand.java:137)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.Node.fireEvent(Node.java:8890)
    at javafx.scene.control.Button.fire(Button.java:203)
    at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:206)
    at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274)
    at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3862)
    at javafx.scene.Scene.processMouseEvent(Scene.java:1849)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2590)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299)
    at java.base/java.security.AccessController.doPrivileged(Unknown Source)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447)
    at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446)
    at com.sun.glass.ui.View.handleMouseEvent(View.java:556)
    at com.sun.glass.ui.View.notifyMouse(View.java:942)
    at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
    at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174)
    at java.base/java.lang.Thread.run(Unknown Source)
INFO: Immune cells: 911
INFO: Stroma: 1306
INFO: Tumor: 3346
INFO: 5563 objects available for classifier training from 1 images
INFO: Classifier training time: 0.22 seconds
INFO: Classification time: 1.19 seconds
INFO: Percentage of correctly classified objects in TRAINING set: 100.00% (n=5563)
WARN: It is *strongly* advised not to report accuracies based on testing using the training set!
INFO: Confusion matrix
                Immune cells          Stroma           Tumor
Immune cells             911               0               0
      Stroma               0            1306               0
       Tumor               0               0            3346

INFO: Number of reclassified objects: 173924 of 668916
ERROR: QuPath exception: 'qupath.lib.gui.helpers.dialogs.DialogHelper qupath.lib.gui.QuPathGUI.getDialogHelper()'
    at qupath.extensions.weka.WekaClassifierCommand.saveWekaData(WekaClassifierCommand.java:192)
    at qupath.extensions.weka.WekaClassifierCommand.lambda$run$1(WekaClassifierCommand.java:137)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.Node.fireEvent(Node.java:8890)
    at javafx.scene.control.Button.fire(Button.java:203)
    at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:206)
    at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274)
    at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3862)
    at javafx.scene.Scene.processMouseEvent(Scene.java:1849)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2590)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299)
    at java.base/java.security.AccessController.doPrivileged(Unknown Source)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447)
    at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446)
    at com.sun.glass.ui.View.handleMouseEvent(View.java:556)
    at com.sun.glass.ui.View.notifyMouse(View.java:942)
    at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
    at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174)
    at java.base/java.lang.Thread.run(Unknown Source)
INFO: Immune cells: 911
INFO: Stroma: 1306
INFO: Tumor: 3346
INFO: 5563 objects available for classifier training from 1 images
INFO: Number of leaves: 5
Size of the tree: 9

INFO: Classifier training time: 0.31 seconds
INFO: Classification time: 1.27 seconds
INFO: Percentage of correctly classified objects in TRAINING set: 99.33% (n=5563)
WARN: It is *strongly* advised not to report accuracies based on testing using the training set!
INFO: Confusion matrix
                Immune cells          Stroma           Tumor
Immune cells             882              29               0
      Stroma               8            1298               0
       Tumor               0               0            3346

INFO: Number of reclassified objects: 205189 of 668916
INFO: Immune cells: 911
INFO: Stroma: 1306
INFO: Tumor: 3346
INFO: 5563 objects available for classifier training from 1 images
INFO: Classifier training time: 0.47 seconds
INFO: Classification time: 4.37 seconds
INFO: Percentage of correctly classified objects in TRAINING set: 99.98% (n=5563)
WARN: It is *strongly* advised not to report accuracies based on testing using the training set!
INFO: Confusion matrix
                Immune cells          Stroma           Tumor
Immune cells             910               1               0
      Stroma               0            1306               0
       Tumor               0               0            3346

INFO: Number of reclassified objects: 157189 of 668916
INFO: Immune cells: 911
INFO: Stroma: 1306
INFO: Tumor: 3346
INFO: 5563 objects available for classifier training from 1 images
INFO: Classifier training time: 0.24 seconds
INFO: Classification time: 1.81 seconds
INFO: Percentage of correctly classified objects in TRAINING set: 100.00% (n=5563)
WARN: It is *strongly* advised not to report accuracies based on testing using the training set!
INFO: Confusion matrix
                Immune cells          Stroma           Tumor
Immune cells             911               0               0
      Stroma               0            1306               0
       Tumor               0               0            3346

INFO: Number of reclassified objects: 63402 of 668916
INFO: Immune cells: 911
INFO: Stroma: 1306
INFO: Tumor: 3346
INFO: 5563 objects available for classifier training from 1 images
INFO: Classifier training time: 0.63 seconds
INFO: Classification time: 4.47 seconds
INFO: Percentage of correctly classified objects in TRAINING set: 100.00% (n=5563)
WARN: It is *strongly* advised not to report accuracies based on testing using the training set!
INFO: Confusion matrix
                Immune cells          Stroma           Tumor
Immune cells             911               0               0
      Stroma               0            1306               0
       Tumor               0               0            3346

INFO: Number of reclassified objects: 63402 of 668916
INFO: Immune cells: 911
INFO: Stroma: 1306
INFO: Tumor: 3346
INFO: 5563 objects available for classifier training from 1 images
INFO: Classifier training time: 0.15 seconds
INFO: Classification time: 1.21 seconds
INFO: Percentage of correctly classified objects in TRAINING set: 100.00% (n=5563)
WARN: It is *strongly* advised not to report accuracies based on testing using the training set!
INFO: Confusion matrix
                Immune cells          Stroma           Tumor
Immune cells             911               0               0
      Stroma               0            1306               0
       Tumor               0               0            3346

INFO: Number of reclassified objects: 173924 of 668916
INFO: Immune cells: 911
INFO: Stroma: 1306
INFO: Tumor: 3346
INFO: 5563 objects available for classifier training from 1 images
INFO: Number of leaves: 5
Size of the tree: 9

INFO: Classifier training time: 0.32 seconds
INFO: Classification time: 1.35 seconds
INFO: Percentage of correctly classified objects in TRAINING set: 99.33% (n=5563)
WARN: It is *strongly* advised not to report accuracies based on testing using the training set!
INFO: Confusion matrix
                Immune cells          Stroma           Tumor
Immune cells             882              29               0
      Stroma               8            1298               0
       Tumor               0               0            3346

INFO: Number of reclassified objects: 205189 of 668916
INFO: Immune cells: 911
INFO: Stroma: 1306
INFO: Tumor: 3346
INFO: 5563 objects available for classifier training from 1 images
INFO: Classifier training time: 0.43 seconds
INFO: Classification time: 7.24 seconds
INFO: Percentage of correctly classified objects in TRAINING set: 99.98% (n=5563)
WARN: It is *strongly* advised not to report accuracies based on testing using the training set!
INFO: Confusion matrix
                Immune cells          Stroma           Tumor
Immune cells             910               1               0
      Stroma               0            1306               0
       Tumor               0               0            3346

INFO: Number of reclassified objects: 157178 of 668916
INFO: Immune cells: 911
INFO: Stroma: 1306
INFO: Tumor: 3346
INFO: 5563 objects available for classifier training from 1 images
INFO: Number of leaves: 5
Size of the tree: 9

INFO: Classifier training time: 0.15 seconds
INFO: Classification time: 1.93 seconds
INFO: Percentage of correctly classified objects in TRAINING set: 99.93% (n=5563)
WARN: It is *strongly* advised not to report accuracies based on testing using the training set!
INFO: Confusion matrix
                Immune cells          Stroma           Tumor
Immune cells             909               2               0
      Stroma               2            1304               0
       Tumor               0               0            3346

INFO: Number of reclassified objects: 157178 of 668916
ERROR: QuPath exception: 'qupath.lib.gui.helpers.dialogs.DialogHelper qupath.lib.gui.QuPathGUI.getDialogHelper()'
    at qupath.extensions.weka.WekaClassifierCommand.saveWekaData(WekaClassifierCommand.java:192)
    at qupath.extensions.weka.WekaClassifierCommand.lambda$run$1(WekaClassifierCommand.java:137)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.Node.fireEvent(Node.java:8890)
    at javafx.scene.control.Button.fire(Button.java:203)
    at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:206)
    at com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274)
    at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218)
    at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
    at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
    at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
    at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
    at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
    at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
    at javafx.event.Event.fireEvent(Event.java:198)
    at javafx.scene.Scene$MouseHandler.process(Scene.java:3862)
    at javafx.scene.Scene.processMouseEvent(Scene.java:1849)
    at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2590)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:409)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:299)
    at java.base/java.security.AccessController.doPrivileged(Unknown Source)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:447)
    at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:412)
    at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:446)
    at com.sun.glass.ui.View.handleMouseEvent(View.java:556)
    at com.sun.glass.ui.View.notifyMouse(View.java:942)
    at com.sun.glass.ui.win.WinApplication._runLoop(Native Method)
    at com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:174)
    at java.base/java.lang.Thread.run(Unknown Source)
petebankhead commented 4 years ago

This extension was written for QuPath v0.1.2 and is not intended to be compatible with v0.2.0-m8 (or v0.2.0 generally). I've updated the readme now to reflect this https://github.com/qupath/qupath-weka-extension/commit/b637e3690cef71b092d00fdbc2cd30a00cd9864a

I plan to rewrite QuPath's object classification for v0.2.0 to make it more powerful and flexible (as mentioned here), and for that reason don't intend to update this extension any time soon.

Potentially a new Weka extension might be created in the future once a stable release of v0.2.0 is available. But I'll close this issue as it's now documented that it is intended to work only with v0.1.2.