{"action":"created","issue":{"url":"https://api.github.com/repos/ignaciorlando/fundus-vessel-segmentation-tbme/issues/4","repository_url":"https://api.github.com/repos/ignaciorlando/fundus-vessel-segmentation-tbme","labels_url":"https://api.github.com/repos/ignaciorlando/fundus-vessel-segmentation-tbme/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/ignaciorlando/fundus-vessel-segmentation-tbme/issues/4/comments","events_url":"https://api.github.com/repos/ignaciorlando/fundus-vessel-segmentation-tbme/issues/4/events","html_url":"https://github.com/ignaciorlando/fundus-vessel-segmentation-tbme/issues/4","id":184123260,"number":4,"title":"how to configure the variable 'thereAreLabelsInTheTestData' in script experiments massive script?","user":{"login":"SevenGong","id":13058184,"avatar_url":"https://avatars.githubusercontent.com/u/13058184?v=3","gravatar_id":"","url":"https://api.github.com/users/SevenGong","html_url":"https://github.com/SevenGong","followers_url":"https://api.github.com/users/SevenGong/followers","following_url":"https://api.github.com/users/SevenGong/following{/other_user}","gists_url":"https://api.github.com/users/SevenGong/gists{/gist_id}","starred_url":"https://api.github.com/users/SevenGong/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SevenGong/subscriptions","organizations_url":"https://api.github.com/users/SevenGong/orgs","repos_url":"https://api.github.com/users/SevenGong/repos","events_url":"https://api.github.com/users/SevenGong/events{/privacy}","received_events_url":"https://api.github.com/users/SevenGong/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-10-20T02:54:53Z","updated_at":"2016-10-20T06:42:57Z","closed_at":null,"body":"I arranged the data sets and modified the corresponding variables, as \r\n   `% Root dir where the data sets are located\r\n    rootDatasets = '/home/xxx/work/vessel/';\r\n    % Root folder where the results are going to be stored variables.The rest are not been changed.\r\n    rootResults = '/home/xxx/work/vessel/results';' \r\nrootDatasets and rootResults are only modified \r\nThen I run the code.But it shows error:\r\n\r\n`Segmenting image number 1/10\r\nSegmenting image number 2/10\r\nSegmenting image number 3/10\r\nSegmenting image number 4/10\r\nSegmenting image number 5/10\r\nSegmenting image number 6/10\r\nSegmenting image number 7/10\r\nSegmenting image number 8/10\r\nSegmenting image number 9/10\r\nSegmenting image number 10/10\r\nReference to non-existent field 'se'.\r\n\r\nError in getAverageMeasures2 (line 9)\r\n    averageQualityMeasures.se = mean(qualityMeasures.se);\r\n\r\n\r\nError in learnCRFPotentials>findBestC (line 74)\r\n            averageMeasures = getAverageMeasures2(currentQualityMeasures);\r\n\r\n\r\nError in learnCRFPotentials (line 16)\r\n        [bestModel, qualityOverValidation, bestParam, ~] = findBestC(config, trainingdata,\r\n        validationdata, better);\r\n\r\n\r\nError in learnConfiguredCRF (line 42)\r\n    [model, qualityOverValidation, config] = learnCRFPotentials(config, trainingdata, validationdata);\r\n\r\n\r\nError in runVesselSegmentation (line 36)\r\n        [model, config.qualityOverValidation, config] = learnConfiguredCRF(trainingdata, validationdata,\r\n        config);\r\n\r\n\r\nError in script_experiments_massive (line 65)\r\n        results{experiment,crfver} = runVesselSegmentation(config);`\r\n\r\nI check and trace the code and find the problem seems to come to the variable 'thereAreLabelsInTheTestData' in script_experiments_massive script? How I handle this problem and run your code correctly? \r\nThank you very much! Looking forward to your reply. "},"comment":{"url":"https://api.github.com/repos/ignaciorlando/fundus-vessel-segmentation-tbme/issues/comments/255022312","html_url":"https://github.com/ignaciorlando/fundus-vessel-segmentation-tbme/issues/4#issuecomment-255022312","issue_url":"https://api.github.com/repos/ignaciorlando/fundus-vessel-segmentation-tbme/issues/4","id":255022312,"user":{"login":"ignaciorlando","id":4671752,"avatar_url":"https://avatars.githubusercontent.com/u/4671752?v=3","gravatar_id":"","url":"https://api.github.com/users/ignaciorlando","html_url":"https://github.com/ignaciorlando","followers_url":"https://api.github.com/users/ignaciorlando/followers","following_url":"https://api.github.com/users/ignaciorlando/following{/other_user}","gists_url":"https://api.github.com/users/ignaciorlando/gists{/gist_id}","starred_url":"https://api.github.com/users/ignaciorlando/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ignaciorlando/subscriptions","organizations_url":"https://api.github.com/users/ignaciorlando/orgs","repos_url":"https://api.github.com/users/ignaciorlando/repos","events_url":"https://api.github.com/users/ignaciorlando/events{/privacy}","received_events_url":"https://api.github.com/users/ignaciorlando/received_events","type":"User","site_admin":false},"created_at":"2016-10-20T06:42:57Z","updated_at":"2016-10-20T06:42:57Z","body":"Hi!\r\n\r\nYour data set folder should have this structure:\r\n- datasetname_folder\r\n-- images\r\n-- masks\r\n-- labels\r\nwhere images contains all the images you want to segment, masks contains their corresponding FOV masks and labels has all their corresponding ground truth annotations. Be sure that every all images within each of the folder are sorted in the same way.\r\n\r\nThe variable thereAreLabelsInTheTestData is hardcoded (yes, I know, that's terrible, I promise I will fix it soon). If your test data has a labels folder, then you can remove that line and replace it by:\r\n\r\n`thereAreLabelsInTheTestData = 1`\r\n\r\nThat should fix the bug. \r\n\r\nGood luck!"}}
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