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container.getMaskBBSize().length can be larger than 3 in CostesSignificanceTest #6

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burgerga opened this Issue Apr 28, 2015 · 3 comments

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burgerga commented Apr 28, 2015

(Fiji Is Just) ImageJ 2.0.0-rc-29/1.49s; Java 1.6.0_24 [64-bit]; Linux 3.13.0-49-generic; 1501MB of 2257MB (66%)

java.lang.ArrayIndexOutOfBoundsException: 3
at algorithms.CostesSignificanceTest.execute(CostesSignificanceTest.java:99)
at Coloc_2.colocalise(Coloc_2.java:447)
at Coloc_2.run(Coloc_2.java:160)
at ij.IJ.runUserPlugIn(IJ.java:199)
at ij.IJ.runPlugIn(IJ.java:163)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:662)

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tomka commented Apr 30, 2015

Thanks for reporting. I'll be able to look into this next week. Do you by any chance have small sample images that trigger this (since I am not able to reproduce)?

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burgerga commented Apr 30, 2015

Unfortunately, I can't give you the real file I worked with. Instead I will give you a modified version where I set all pixel values to 1 and then cropped the image to a reasonable size, you can find it here: https://gist.github.com/burgerga/db94e602aa67b93bcc3d#file-synthetic_small-ome

Steps to reproduce:

  • Open in Fiji
  • Image > Color > Split channel
  • Analyze > Colocalization -> Coloc 2
    • Unselect all algorithms except "Costes' Significance Test"
    • Press OK

@ctrueden ctrueden added this to the m1 milestone Jul 29, 2015

@chalkie666 chalkie666 added the bug label Jul 30, 2015

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chalkie666 commented Jul 30, 2015

time series data will trigger this bug
eg sample images - mitosis.tif
it makes no sense to do analysis on a time series... each time point must be analysed separately. So we should detect if imagej says the image is a time series, warn the user and quit. Or process each timepoint separately and set the jobName for each timepoint accordingly for the results. THe latter is probably what the naive user expects.

(you could imagine doing a correlation measurement between different time points of the same colour channel.... then the images would need to be shuffled in dimensions appropriately, or a fancy input GUI created to select which dimensions to correlate against which...)

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