{"action":"created","issue":{"url":"https://api.github.com/repos/fiji/Colocalisation_Analysis/issues/37","labels_url":"https://api.github.com/repos/fiji/Colocalisation_Analysis/issues/37/labels{/name}","comments_url":"https://api.github.com/repos/fiji/Colocalisation_Analysis/issues/37/comments","events_url":"https://api.github.com/repos/fiji/Colocalisation_Analysis/issues/37/events","html_url":"https://github.com/fiji/Colocalisation_Analysis/issues/37","id":101379905,"number":37,"title":"Algorithms: ArrayIndex  out of bounds: 512x512x46 px, 32 bit images input (184 MB)","user":{"login":"chalkie666","id":259634,"avatar_url":"https://avatars.githubusercontent.com/u/259634?v=3","gravatar_id":"","url":"https://api.github.com/users/chalkie666","html_url":"https://github.com/chalkie666","followers_url":"https://api.github.com/users/chalkie666/followers","following_url":"https://api.github.com/users/chalkie666/following{/other_user}","gists_url":"https://api.github.com/users/chalkie666/gists{/gist_id}","starred_url":"https://api.github.com/users/chalkie666/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chalkie666/subscriptions","organizations_url":"https://api.github.com/users/chalkie666/orgs","repos_url":"https://api.github.com/users/chalkie666/repos","events_url":"https://api.github.com/users/chalkie666/events{/privacy}","received_events_url":"https://api.github.com/users/chalkie666/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/fiji/Colocalisation_Analysis/labels/bug","name":"bug","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/fiji/Colocalisation_Analysis/milestones/2","html_url":"https://github.com/fiji/Colocalisation_Analysis/milestones/m1","labels_url":"https://api.github.com/repos/fiji/Colocalisation_Analysis/milestones/2/labels","id":1232051,"number":2,"title":"m1","description":"","creator":{"login":"ctrueden","id":556626,"avatar_url":"https://avatars.githubusercontent.com/u/556626?v=3","gravatar_id":"","url":"https://api.github.com/users/ctrueden","html_url":"https://github.com/ctrueden","followers_url":"https://api.github.com/users/ctrueden/followers","following_url":"https://api.github.com/users/ctrueden/following{/other_user}","gists_url":"https://api.github.com/users/ctrueden/gists{/gist_id}","starred_url":"https://api.github.com/users/ctrueden/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ctrueden/subscriptions","organizations_url":"https://api.github.com/users/ctrueden/orgs","repos_url":"https://api.github.com/users/ctrueden/repos","events_url":"https://api.github.com/users/ctrueden/events{/privacy}","received_events_url":"https://api.github.com/users/ctrueden/received_events","type":"User","site_admin":false},"open_issues":7,"closed_issues":1,"state":"open","created_at":"2015-07-29T17:38:56Z","updated_at":"2015-08-17T09:40:27Z","due_on":null,"closed_at":null},"comments":2,"created_at":"2015-08-17T09:40:27Z","updated_at":"2015-08-17T13:36:14Z","closed_at":null,"body":"@ctrueden an opinion would be great here... then i will do as needed. \r\n\r\ntwo input images - quite large: \r\n512x512x46 px, 32 bit  (184 MB)\r\n\r\nLooks like a long isnt big enough to count all the pixels?????\r\nShould we use BigInteger?\r\n\r\nrun coloc_2, in 2D Histograms  step get: \r\n\r\n(Fiji Is Just) ImageJ 2.0.0-rc-34/1.50a; Java 1.7.0_79 [64-bit]; Linux 3.19.0-21-generic; 2132MB of 2421MB (88%)\r\n \r\njava.lang.ArrayIndexOutOfBoundsException: 65538\r\n\tat net.imglib2.img.basictypeaccess.array.LongArray.getValue(LongArray.java:63)\r\n\tat net.imglib2.type.numeric.integer.LongType.get(LongType.java:116)\r\n\tat net.imglib2.type.numeric.integer.LongType.getIntegerLong(LongType.java:133)\r\n\tat algorithms.Histogram2D.generateHistogramData(Histogram2D.java:207)\r\n\tat algorithms.LiHistogram2D.execute(LiHistogram2D.java:95)\r\n\tat Coloc_2.colocalise(Coloc_2.java:447)\r\n\tat Coloc_2.run(Coloc_2.java:160)\r\n\tat ij.IJ.runUserPlugIn(IJ.java:212)\r\n\tat ij.IJ.runPlugIn(IJ.java:176)\r\n\tat ij.Executer.runCommand(Executer.java:132)\r\n\tat ij.Executer.run(Executer.java:65)\r\n\tat java.lang.Thread.run(Thread.java:745)\r\n"},"comment":{"url":"https://api.github.com/repos/fiji/Colocalisation_Analysis/issues/comments/131819745","html_url":"https://github.com/fiji/Colocalisation_Analysis/issues/37#issuecomment-131819745","issue_url":"https://api.github.com/repos/fiji/Colocalisation_Analysis/issues/37","id":131819745,"user":{"login":"chalkie666","id":259634,"avatar_url":"https://avatars.githubusercontent.com/u/259634?v=3","gravatar_id":"","url":"https://api.github.com/users/chalkie666","html_url":"https://github.com/chalkie666","followers_url":"https://api.github.com/users/chalkie666/followers","following_url":"https://api.github.com/users/chalkie666/following{/other_user}","gists_url":"https://api.github.com/users/chalkie666/gists{/gist_id}","starred_url":"https://api.github.com/users/chalkie666/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chalkie666/subscriptions","organizations_url":"https://api.github.com/users/chalkie666/orgs","repos_url":"https://api.github.com/users/chalkie666/repos","events_url":"https://api.github.com/users/chalkie666/events{/privacy}","received_events_url":"https://api.github.com/users/chalkie666/received_events","type":"User","site_admin":false},"created_at":"2015-08-17T13:36:14Z","updated_at":"2015-08-17T13:36:14Z","body":"hmmmmm, I don't  get why getXValue could be returning a bad value that doesnt fit in a the long data type. Its getting the number from imglib2   : \r\n\r\n207:     long count = histogram2DCursor.get().getIntegerLong();\r\n\r\nis getting the vlaue of the 2D histogram image we are contructing at that pair of x y histogram image coordinates... so we can increment it by 1. \r\n\r\njava.lang.ArrayIndexOutOfBoundsException: 65538\r\nat net.imglib2.img.basictypeaccess.array.LongArray.getValue(LongArray.java:63)\r\n..........\r\n\r\n65538 is suspiciously close to the 16 bit limit...  but a long is +- 2 pow 63\r\nor am i on totally the wrong track here? \r\n\r\nI need to learn how imglib2 really does this data access....."}}