{"action":"created","issue":{"url":"https://api.github.com/repos/OPIC-Oxford/localrec/issues/4","repository_url":"https://api.github.com/repos/OPIC-Oxford/localrec","labels_url":"https://api.github.com/repos/OPIC-Oxford/localrec/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/OPIC-Oxford/localrec/issues/4/comments","events_url":"https://api.github.com/repos/OPIC-Oxford/localrec/issues/4/events","html_url":"https://github.com/OPIC-Oxford/localrec/pull/4","id":165987906,"number":4,"title":"Using Scipion ImageHandler to write individual images","user":{"login":"delarosatrevin","id":8441688,"avatar_url":"https://avatars.githubusercontent.com/u/8441688?v=3","gravatar_id":"","url":"https://api.github.com/users/delarosatrevin","html_url":"https://github.com/delarosatrevin","followers_url":"https://api.github.com/users/delarosatrevin/followers","following_url":"https://api.github.com/users/delarosatrevin/following{/other_user}","gists_url":"https://api.github.com/users/delarosatrevin/gists{/gist_id}","starred_url":"https://api.github.com/users/delarosatrevin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/delarosatrevin/subscriptions","organizations_url":"https://api.github.com/users/delarosatrevin/orgs","repos_url":"https://api.github.com/users/delarosatrevin/repos","events_url":"https://api.github.com/users/delarosatrevin/events{/privacy}","received_events_url":"https://api.github.com/users/delarosatrevin/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":{"login":"JuhaHuiskonen","id":20352352,"avatar_url":"https://avatars.githubusercontent.com/u/20352352?v=3","gravatar_id":"","url":"https://api.github.com/users/JuhaHuiskonen","html_url":"https://github.com/JuhaHuiskonen","followers_url":"https://api.github.com/users/JuhaHuiskonen/followers","following_url":"https://api.github.com/users/JuhaHuiskonen/following{/other_user}","gists_url":"https://api.github.com/users/JuhaHuiskonen/gists{/gist_id}","starred_url":"https://api.github.com/users/JuhaHuiskonen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JuhaHuiskonen/subscriptions","organizations_url":"https://api.github.com/users/JuhaHuiskonen/orgs","repos_url":"https://api.github.com/users/JuhaHuiskonen/repos","events_url":"https://api.github.com/users/JuhaHuiskonen/events{/privacy}","received_events_url":"https://api.github.com/users/JuhaHuiskonen/received_events","type":"User","site_admin":false},"assignees":[{"login":"JuhaHuiskonen","id":20352352,"avatar_url":"https://avatars.githubusercontent.com/u/20352352?v=3","gravatar_id":"","url":"https://api.github.com/users/JuhaHuiskonen","html_url":"https://github.com/JuhaHuiskonen","followers_url":"https://api.github.com/users/JuhaHuiskonen/followers","following_url":"https://api.github.com/users/JuhaHuiskonen/following{/other_user}","gists_url":"https://api.github.com/users/JuhaHuiskonen/gists{/gist_id}","starred_url":"https://api.github.com/users/JuhaHuiskonen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JuhaHuiskonen/subscriptions","organizations_url":"https://api.github.com/users/JuhaHuiskonen/orgs","repos_url":"https://api.github.com/users/JuhaHuiskonen/repos","events_url":"https://api.github.com/users/JuhaHuiskonen/events{/privacy}","received_events_url":"https://api.github.com/users/JuhaHuiskonen/received_events","type":"User","site_admin":false}],"milestone":null,"comments":1,"created_at":"2016-07-17T18:03:07Z","updated_at":"2016-07-18T07:05:15Z","closed_at":"2016-07-18T07:05:15Z","pull_request":{"url":"https://api.github.com/repos/OPIC-Oxford/localrec/pulls/4","html_url":"https://github.com/OPIC-Oxford/localrec/pull/4","diff_url":"https://github.com/OPIC-Oxford/localrec/pull/4.diff","patch_url":"https://github.com/OPIC-Oxford/localrec/pull/4.patch"},"body":"This is just an idea to use Scipion ImageHandler class to deal with stack splitting and writing of individual images. \r\n\r\nFor  this to work you should run the main script with 'scipion python ...' prefix. But I guess it is not a big deal if you were thinking in already use 'scipion xmipp_image_convert ...' command. \r\n\r\nThis variant have two main advantages: (a) You do not spawn a new process just to split the stack, and (b) You can skip the trick to create the empty mask to write particles as separate .mrc files. Plus the bonus that you totally remove the 'bsoft' dependency.\r\n\r\nMoreover, now Scipion uses the underlying Xmipp Image class, but in a future we plan to separate into a library. So conceptually, this new way does not even depend on Xmipp. \r\n\r\nHaving said that, I haven't test these new changes, so it is only a prototype. I just created the Pull Request for you to clearly see the differences."},"comment":{"url":"https://api.github.com/repos/OPIC-Oxford/localrec/issues/comments/233249555","html_url":"https://github.com/OPIC-Oxford/localrec/pull/4#issuecomment-233249555","issue_url":"https://api.github.com/repos/OPIC-Oxford/localrec/issues/4","id":233249555,"user":{"login":"JuhaHuiskonen","id":20352352,"avatar_url":"https://avatars.githubusercontent.com/u/20352352?v=3","gravatar_id":"","url":"https://api.github.com/users/JuhaHuiskonen","html_url":"https://github.com/JuhaHuiskonen","followers_url":"https://api.github.com/users/JuhaHuiskonen/followers","following_url":"https://api.github.com/users/JuhaHuiskonen/following{/other_user}","gists_url":"https://api.github.com/users/JuhaHuiskonen/gists{/gist_id}","starred_url":"https://api.github.com/users/JuhaHuiskonen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JuhaHuiskonen/subscriptions","organizations_url":"https://api.github.com/users/JuhaHuiskonen/orgs","repos_url":"https://api.github.com/users/JuhaHuiskonen/repos","events_url":"https://api.github.com/users/JuhaHuiskonen/events{/privacy}","received_events_url":"https://api.github.com/users/JuhaHuiskonen/received_events","type":"User","site_admin":false},"created_at":"2016-07-18T07:05:15Z","updated_at":"2016-07-18T07:05:15Z","body":"Thanks a lot, I will merge and test."}}
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