{"action":"created","issue":{"url":"https://api.github.com/repos/ehodneland/cellsegm/issues/3","labels_url":"https://api.github.com/repos/ehodneland/cellsegm/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/ehodneland/cellsegm/issues/3/comments","events_url":"https://api.github.com/repos/ehodneland/cellsegm/issues/3/events","html_url":"https://github.com/ehodneland/cellsegm/issues/3","id":115007606,"number":3,"title":"Examples not working","user":{"login":"DarkCellAD","id":4184907,"avatar_url":"https://avatars.githubusercontent.com/u/4184907?v=3","gravatar_id":"","url":"https://api.github.com/users/DarkCellAD","html_url":"https://github.com/DarkCellAD","followers_url":"https://api.github.com/users/DarkCellAD/followers","following_url":"https://api.github.com/users/DarkCellAD/following{/other_user}","gists_url":"https://api.github.com/users/DarkCellAD/gists{/gist_id}","starred_url":"https://api.github.com/users/DarkCellAD/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DarkCellAD/subscriptions","organizations_url":"https://api.github.com/users/DarkCellAD/orgs","repos_url":"https://api.github.com/users/DarkCellAD/repos","events_url":"https://api.github.com/users/DarkCellAD/events{/privacy}","received_events_url":"https://api.github.com/users/DarkCellAD/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-11-04T09:22:01Z","updated_at":"2015-11-04T13:25:45Z","closed_at":null,"body":"In all the latest ~10 commits I cannot seem to get the examples to work. (I only tried 3D examples but none worked) They exit with various errors from missing functions over index mismatches to missing input arguments. Hence I cannot really try out the code to get it to work for me.\r\nI'm working on Matlab 2015b.\r\nFor the latest commit:\r\nExample \"surf stain_3D\"\r\n\r\nIndex exceeds matrix dimensions.\r\n\r\nError in gaussian (line 59)\r\n    g = (1/n)*exp(-(1/2)*(sigmainv(1,1)*x{1}.^2 + sigmainv(2,2)*x{2}.^2 +\r\n    sigmainv(3,3)*x{3}.^2));\r\n\r\nError in cellsegm.ridgeenhhessian (line 68)\r\ng1 = gaussian(dim,prm.stdev);\r\n\r\nError in cellsegm.segmsurf (line 323)\r\n    imsegm = cellsegm.ridgeenhhessian(imsegm,prm.h);\r\n\r\nError in surfstain_3D (line 41)\r\n    cellsegm.segmsurf(imsegm,20,100,'prm',prm);\r\n\r\n\r\nExample \"surfstain_and_nucleus_3D\"\r\n\r\nNot enough input arguments.\r\n\r\nError in ball (line 20)\r\n        if length(size) == 1,\r\n\r\nError in cellsegm.segmct>segmthrs (line 624)\r\n    load ball1;se = getball(ball,1,1);\r\n\r\nError in cellsegm.segmct (line 213)\r\n    [cellbw] = segmthrs(im,prmin,conn);\r\n\r\nError in cellsegm.getminima>nucleus (line 440)\r\n[minimahere,wat] =\r\ncellsegm.segmct(imhere,0.1*prm.minvolfull/1000,prm.maxvolfull/1000,'prm',prmin);\r\n\r\nError in cellsegm.getminima (line 219)\r\n    minimacell = nucleus(imnucl,prmin);\r\n\r\nError in cellsegm.segmsurf (line 355)\r\n        [minima,minimacell,prmout] =\r\n        cellsegm.getminima(imsegm,minimacell,prmin,imnucl);\r\n\r\nError in surfstain_and_nucleus_3D (line 47)\r\n    cellsegm.segmsurf(imsegm,3,100,'imnucleus',imnucl,'prm',prm);\r\n\r\n\r\nExample \"tissue_3D\"\r\n\r\nUnable to load ../data/tissue/stack3\r\nUnable to read file '../data/tissue/stack3'. No such file or directory.\r\nCould not load ../data/tissue/stack3, continuing\r\nUnable to load ../data/tissue/stack4\r\nUnable to read file '../data/tissue/stack4'. No such file or directory.\r\nCould not load ../data/tissue/stack4, continuing"},"comment":{"url":"https://api.github.com/repos/ehodneland/cellsegm/issues/comments/153718683","html_url":"https://github.com/ehodneland/cellsegm/issues/3#issuecomment-153718683","issue_url":"https://api.github.com/repos/ehodneland/cellsegm/issues/3","id":153718683,"user":{"login":"ehodneland","id":5240155,"avatar_url":"https://avatars.githubusercontent.com/u/5240155?v=3","gravatar_id":"","url":"https://api.github.com/users/ehodneland","html_url":"https://github.com/ehodneland","followers_url":"https://api.github.com/users/ehodneland/followers","following_url":"https://api.github.com/users/ehodneland/following{/other_user}","gists_url":"https://api.github.com/users/ehodneland/gists{/gist_id}","starred_url":"https://api.github.com/users/ehodneland/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ehodneland/subscriptions","organizations_url":"https://api.github.com/users/ehodneland/orgs","repos_url":"https://api.github.com/users/ehodneland/repos","events_url":"https://api.github.com/users/ehodneland/events{/privacy}","received_events_url":"https://api.github.com/users/ehodneland/received_events","type":"User","site_admin":false},"created_at":"2015-11-04T13:25:45Z","updated_at":"2015-11-04T13:25:45Z","body":"Hi,\n\nif you pull the latest version the bug should be fixed. Regarding the \nlast error message\nUnable to load ../data/tissue/stack3\nUnable to read file '../data/tissue/stack3'. No such file or directory.\nCould not load ../data/tissue/stack3, continuing\nUnable to load ../data/tissue/stack4\nUnable to read file '../data/tissue/stack4'. No such file or directory.\nCould not load ../data/tissue/stack4, continuing\n\nmake sure that you have downloaded the given data as well, in \n../data/tissue/ (provided you are running the examples from the example \nfolder)\n\nBest regards\n\nErlend Hodneland\n\nOn 11/4/15 10:22 AM, DarkCellAD wrote:\n>\n> In all the latest ~10 commits I cannot seem to get the examples to \n> work. (I only tried 3D examples but none worked) They exit with \n> various errors from missing functions over index mismatches to missing \n> input arguments. Hence I cannot really try out the code to get it to \n> work for me.\n> I'm working on Matlab 2015b.\n> For the latest commit:\n> Example \"surf stain_3D\"\n>\n> Index exceeds matrix dimensions.\n>\n> Error in gaussian (line 59)\n> g = (1/n)/exp(-(1/2)/(sigmainv(1,1)/x{1}.^2 + sigmainv(2,2)/x{2}.^2 +\n> sigmainv(3,3)*x{3}.^2));\n>\n> Error in cellsegm.ridgeenhhessian (line 68)\n> g1 = gaussian(dim,prm.stdev);\n>\n> Error in cellsegm.segmsurf (line 323)\n> imsegm = cellsegm.ridgeenhhessian(imsegm,prm.h);\n>\n> Error in surfstain_3D (line 41)\n> cellsegm.segmsurf(imsegm,20,100,'prm',prm);\n>\n> Example \"surfstain_and_nucleus_3D\"\n>\n> Not enough input arguments.\n>\n> Error in ball (line 20)\n> if length(size) == 1,\n>\n> Error in cellsegm.segmct>segmthrs (line 624)\n> load ball1;se = getball(ball,1,1);\n>\n> Error in cellsegm.segmct (line 213)\n> [cellbw] = segmthrs(im,prmin,conn);\n>\n> Error in cellsegm.getminima>nucleus (line 440)\n> [minimahere,wat] =\n> cellsegm.segmct(imhere,0.1*prm.minvolfull/1000,prm.maxvolfull/1000,'prm',prmin);\n>\n> Error in cellsegm.getminima (line 219)\n> minimacell = nucleus(imnucl,prmin);\n>\n> Error in cellsegm.segmsurf (line 355)\n> [minima,minimacell,prmout] =\n> cellsegm.getminima(imsegm,minimacell,prmin,imnucl);\n>\n> Error in surfstain_and_nucleus_3D (line 47)\n> cellsegm.segmsurf(imsegm,3,100,'imnucleus',imnucl,'prm',prm);\n>\n> Example \"tissue_3D\"\n>\n> Unable to load ../data/tissue/stack3\n> Unable to read file '../data/tissue/stack3'. No such file or directory.\n> Could not load ../data/tissue/stack3, continuing\n> Unable to load ../data/tissue/stack4\n> Unable to read file '../data/tissue/stack4'. No such file or directory.\n> Could not load ../data/tissue/stack4, continuing\n>\n> —\n> Reply to this email directly or view it on GitHub \n> <https://github.com/ehodneland/cellsegm/issues/3>.\n>\n\n"}}