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I2PC / scipion

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)
http://scipion.i2pc.es
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Java exception when changing the boxsize in the Picking GUI #1233

Closed delarosatrevin closed 5 years ago

delarosatrevin commented 6 years ago

@pconesa I think after you changes in the picking there is an Exception when changing the box size.

java -Xmx2g -d64 -Djava.library.path=/home/josem/work/development/scipion/software/em/xmipp/lib -Dplugins.dir=/home/josem/work/development/scipion/software/em/xmipp/external/imagej/plugins -cp /usr/lib/jvm/java-8-openjdk-amd64/lib/:/home/josem/work/development/scipion/software/em/xmipp/external/imagej/:/home/josem/work/development/scipion/software/em/xmipp/java/lib/* xmipp.viewer.particlepicker.training.SupervisedPickerRunner --input ./Tmp/8746.outputMicrographsDoseWeighted_micrographs.xmd --output ./Tmp/8854.outputCoordinates --scipion 60553 --tmp true Oct 02, 2017 8:31:33 AM xmipp.viewer.particlepicker.training.model.ManualParticle loadImagePlus SEVERE: null java.lang.ArrayIndexOutOfBoundsException: 9768960 at ij.process.FloatProcessor.crop(FloatProcessor.java:727) at xmipp.viewer.particlepicker.training.model.ManualParticle.loadImagePlus(ManualParticle.java:81) at xmipp.viewer.particlepicker.training.model.ManualParticle.getImageGeneric(ManualParticle.java:114) at xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker$UpdateTemplatesTask.doInBackground(SupervisedParticlePicker.java:1298) at xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker$UpdateTemplatesTask.doInBackground(SupervisedParticlePicker.java:1249) at javax.swing.SwingWorker$1.call(SwingWorker.java:295) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at javax.swing.SwingWorker.run(SwingWorker.java:334) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

java.lang.IllegalArgumentException: 9768960 at xmipp.viewer.particlepicker.training.model.ManualParticle.loadImagePlus(ManualParticle.java:87) at xmipp.viewer.particlepicker.training.model.ManualParticle.getImageGeneric(ManualParticle.java:114) at xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker$UpdateTemplatesTask.doInBackground(SupervisedParticlePicker.java:1298) at xmipp.viewer.particlepicker.training.model.SupervisedParticlePicker$UpdateTemplatesTask.doInBackground(SupervisedParticlePicker.java:1249) at javax.swing.SwingWorker$1.call(SwingWorker.java:295) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at javax.swing.SwingWorker.run(SwingWorker.java:334) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

pconesa commented 6 years ago

Always?, Did you have an ongoing training? Nevertheless I'll have a look. Thanks.

pconesa commented 6 years ago

Not able to reproduce it...any specific sequence. I guess you where picking in tmp....after analyze result?

pconesa commented 6 years ago

@delarosatrevin , have you seen this again?

pconesa commented 6 years ago

@delarosatrevin , anyway I can reproduce this?

pconesa commented 5 years ago

I'm closing this issue. I've made some changes and never got this exception. Feel free to reopen it.