{"action":"created","issue":{"url":"https://api.github.com/repos/STScI-JWST/jwst/issues/841","repository_url":"https://api.github.com/repos/STScI-JWST/jwst","labels_url":"https://api.github.com/repos/STScI-JWST/jwst/issues/841/labels{/name}","comments_url":"https://api.github.com/repos/STScI-JWST/jwst/issues/841/comments","events_url":"https://api.github.com/repos/STScI-JWST/jwst/issues/841/events","html_url":"https://github.com/STScI-JWST/jwst/issues/841","id":224491104,"number":841,"title":"Need to flag reference pixels for excluding from image combination","user":{"login":"hbushouse","id":12860084,"avatar_url":"https://avatars1.githubusercontent.com/u/12860084?v=4","gravatar_id":"","url":"https://api.github.com/users/hbushouse","html_url":"https://github.com/hbushouse","followers_url":"https://api.github.com/users/hbushouse/followers","following_url":"https://api.github.com/users/hbushouse/following{/other_user}","gists_url":"https://api.github.com/users/hbushouse/gists{/gist_id}","starred_url":"https://api.github.com/users/hbushouse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hbushouse/subscriptions","organizations_url":"https://api.github.com/users/hbushouse/orgs","repos_url":"https://api.github.com/users/hbushouse/repos","events_url":"https://api.github.com/users/hbushouse/events{/privacy}","received_events_url":"https://api.github.com/users/hbushouse/received_events","type":"User","site_admin":false},"labels":[{"id":390242605,"url":"https://api.github.com/repos/STScI-JWST/jwst/labels/dq_init","name":"dq_init","color":"fbca04","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/STScI-JWST/jwst/milestones/3","html_url":"https://github.com/STScI-JWST/jwst/milestone/3","labels_url":"https://api.github.com/repos/STScI-JWST/jwst/milestones/3/labels","id":2066506,"number":3,"title":"Build 7.1","description":"JWST Pipeline Build 7.1","creator":{"login":"hbushouse","id":12860084,"avatar_url":"https://avatars1.githubusercontent.com/u/12860084?v=4","gravatar_id":"","url":"https://api.github.com/users/hbushouse","html_url":"https://github.com/hbushouse","followers_url":"https://api.github.com/users/hbushouse/followers","following_url":"https://api.github.com/users/hbushouse/following{/other_user}","gists_url":"https://api.github.com/users/hbushouse/gists{/gist_id}","starred_url":"https://api.github.com/users/hbushouse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hbushouse/subscriptions","organizations_url":"https://api.github.com/users/hbushouse/orgs","repos_url":"https://api.github.com/users/hbushouse/repos","events_url":"https://api.github.com/users/hbushouse/events{/privacy}","received_events_url":"https://api.github.com/users/hbushouse/received_events","type":"User","site_admin":false},"open_issues":106,"closed_issues":310,"state":"open","created_at":"2016-10-13T00:22:25Z","updated_at":"2017-08-23T12:11:30Z","due_on":"2017-09-30T07:00:00Z","closed_at":null},"comments":0,"created_at":"2017-04-26T14:38:43Z","updated_at":"2017-08-23T13:26:58Z","closed_at":null,"body":"The reference pixels for all detectors need to be excluded from use when doing operations like combining multiple images into a mosaic. The easiest way to get them excluded is to have a unique DQ flag value set for them. The current set of standard flags includes:\r\n\r\n'DO_NOT_USE': 1\r\n'NON_SCIENCE': 512\r\n\r\nso perhaps one (or both) of those values could be used. \r\n\r\nIn addition to reference pixels, various areas of the MIRI Imaging detector also need to be flagged when they aren't useful for the current exp_type. For example, when the exposure is for direct imaging (MIR_IMAGE), all areas outside of the imaging portion of the FOV need to be flagged.\r\n\r\nThe logical (in my opinion) place to introduce these flags into the pipeline flow is to have them set in the MASK reference file that gets loaded by the dq_init step. That of course means we need to have the instrument teams deliver updated MASK files containing these flags."},"comment":{"url":"https://api.github.com/repos/STScI-JWST/jwst/issues/comments/324330521","html_url":"https://github.com/STScI-JWST/jwst/issues/841#issuecomment-324330521","issue_url":"https://api.github.com/repos/STScI-JWST/jwst/issues/841","id":324330521,"user":{"login":"hbushouse","id":12860084,"avatar_url":"https://avatars1.githubusercontent.com/u/12860084?v=4","gravatar_id":"","url":"https://api.github.com/users/hbushouse","html_url":"https://github.com/hbushouse","followers_url":"https://api.github.com/users/hbushouse/followers","following_url":"https://api.github.com/users/hbushouse/following{/other_user}","gists_url":"https://api.github.com/users/hbushouse/gists{/gist_id}","starred_url":"https://api.github.com/users/hbushouse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hbushouse/subscriptions","organizations_url":"https://api.github.com/users/hbushouse/orgs","repos_url":"https://api.github.com/users/hbushouse/repos","events_url":"https://api.github.com/users/hbushouse/events{/privacy}","received_events_url":"https://api.github.com/users/hbushouse/received_events","type":"User","site_admin":false},"created_at":"2017-08-23T13:26:58Z","updated_at":"2017-08-23T13:26:58Z","body":"During the 15 Aug 2017 meeting of the JCCWG (https://confluence.stsci.edu/display/JWSTCC/2017-08-15+Meeting+notes) it was decided that the instrument teams would update their MASK reference files to flag reference pixels with a new DQ flag value to indicate that they are reference pixels. Hence we need to define a new DQ flag value (REFERENCE_PIXEL) for this condition and then update any routines (e.g. resample) that need to discard pixels based on this flag.\r\n\r\nNote that this still does not solve the issue of MIRI imaging exposures that include regions of the LRS spectrometer and coronagraphic masks. Can this be handled in some way via something like bounding boxes in the WCS?"}}
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