{"action":"created","issue":{"url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/97","repository_url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues","labels_url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/97/labels{/name}","comments_url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/97/comments","events_url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/97/events","html_url":"https://github.com/cryoem-uoft/cryosparc-issues/issues/97","id":195677854,"number":97,"title":"Contrast getting inverted for refinement","user":{"login":"mbrubake","id":3383416,"avatar_url":"https://avatars.githubusercontent.com/u/3383416?v=3","gravatar_id":"","url":"https://api.github.com/users/mbrubake","html_url":"https://github.com/mbrubake","followers_url":"https://api.github.com/users/mbrubake/followers","following_url":"https://api.github.com/users/mbrubake/following{/other_user}","gists_url":"https://api.github.com/users/mbrubake/gists{/gist_id}","starred_url":"https://api.github.com/users/mbrubake/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mbrubake/subscriptions","organizations_url":"https://api.github.com/users/mbrubake/orgs","repos_url":"https://api.github.com/users/mbrubake/repos","events_url":"https://api.github.com/users/mbrubake/events{/privacy}","received_events_url":"https://api.github.com/users/mbrubake/received_events","type":"User","site_admin":false},"labels":[{"id":334421756,"url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/labels/bug","name":"bug","color":"eb6420","default":true},{"id":334449757,"url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/labels/urgent","name":"urgent","color":"e11d21","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":33,"created_at":"2016-12-14T23:43:09Z","updated_at":"2016-12-22T20:50:05Z","closed_at":null,"body":"Two different users with two different datasets have seen contrast get inverted for refinement.  In both cases the dataset sign appears to be set correctly and ab initio runs appear to work fine but when switching to refinement, the map gets flipped. @zrip @johnrubinstein @alipunjani Has anyone else seen this kind of behaviour?  There's very little consistency.  One was with a PAR file, another was with a STAR file.  Flipping the datasign doesn't fix things either."},"comment":{"url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/comments/268887675","html_url":"https://github.com/cryoem-uoft/cryosparc-issues/issues/97#issuecomment-268887675","issue_url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/97","id":268887675,"user":{"login":"mbrubake","id":3383416,"avatar_url":"https://avatars.githubusercontent.com/u/3383416?v=3","gravatar_id":"","url":"https://api.github.com/users/mbrubake","html_url":"https://github.com/mbrubake","followers_url":"https://api.github.com/users/mbrubake/followers","following_url":"https://api.github.com/users/mbrubake/following{/other_user}","gists_url":"https://api.github.com/users/mbrubake/gists{/gist_id}","starred_url":"https://api.github.com/users/mbrubake/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mbrubake/subscriptions","organizations_url":"https://api.github.com/users/mbrubake/orgs","repos_url":"https://api.github.com/users/mbrubake/repos","events_url":"https://api.github.com/users/mbrubake/events{/privacy}","received_events_url":"https://api.github.com/users/mbrubake/received_events","type":"User","site_admin":false},"created_at":"2016-12-22T20:50:04Z","updated_at":"2016-12-22T20:50:04Z","body":"Wow, good catch!  Does it only happen with ifft or does it happen with fft as well?  If this is the root cause then it has to only occur with ifft, because in ab initio the image size is still the full box size.\r\n\r\n@chesh-ohsu @snoreng Can you tell us the box size for your datasets so we can check if this might be the common cause?"}}
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