{"action":"created","issue":{"url":"https://api.github.com/repos/Keck-DataReductionPipelines/MosfireDRP/issues/35","labels_url":"https://api.github.com/repos/Keck-DataReductionPipelines/MosfireDRP/issues/35/labels{/name}","comments_url":"https://api.github.com/repos/Keck-DataReductionPipelines/MosfireDRP/issues/35/comments","events_url":"https://api.github.com/repos/Keck-DataReductionPipelines/MosfireDRP/issues/35/events","html_url":"https://github.com/Keck-DataReductionPipelines/MosfireDRP/issues/35","id":109712911,"number":35,"title":"Final combined rectified spectrum has additional noise","user":{"login":"followthesheep","id":3268415,"avatar_url":"https://avatars.githubusercontent.com/u/3268415?v=3","gravatar_id":"","url":"https://api.github.com/users/followthesheep","html_url":"https://github.com/followthesheep","followers_url":"https://api.github.com/users/followthesheep/followers","following_url":"https://api.github.com/users/followthesheep/following{/other_user}","gists_url":"https://api.github.com/users/followthesheep/gists{/gist_id}","starred_url":"https://api.github.com/users/followthesheep/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/followthesheep/subscriptions","organizations_url":"https://api.github.com/users/followthesheep/orgs","repos_url":"https://api.github.com/users/followthesheep/repos","events_url":"https://api.github.com/users/followthesheep/events{/privacy}","received_events_url":"https://api.github.com/users/followthesheep/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":14,"created_at":"2015-10-04T23:33:02Z","updated_at":"2015-11-02T18:07:27Z","closed_at":null,"body":"The final combined and rectified FITS file seems to have a lot of bad pixels. I've attached a plot below comparing the extraction of a spectrum from Background.handle_background() (blue) compared to from the final step of Rectify.handle_rectification() (green). \r\n\r\n![mosfire_spec_compare](https://cloud.githubusercontent.com/assets/3268415/10270862/2dee344a-6ab4-11e5-9f1d-1886a8797dac.png)\r\n\r\nI think the maybe the combination of the images at the end somehow is propagating bad pixels of each frame into the last one. \r\n\r\nhip 109452_rectified_H_A-B.fits: \r\nhttps://drive.google.com/file/d/0B_YkzZoUSrX-ZWtBbVZXWlZWUWM/view?usp=sharing \r\nhip 109452_H_long_eps.fits:\r\nhttps://drive.google.com/file/d/0B_YkzZoUSrX-OVVOWDJQdUVDUjQ/view?usp=sharing\r\n\r\n\r\nThe spectrum above is a standard star. There are six frames in it. CRR removal I think is being done with min/max rejection. I've been seeing this in my science data too, though the SNR is not as high, so it is not as apparent. \r\n\r\n"},"comment":{"url":"https://api.github.com/repos/Keck-DataReductionPipelines/MosfireDRP/issues/comments/153104392","html_url":"https://github.com/Keck-DataReductionPipelines/MosfireDRP/issues/35#issuecomment-153104392","issue_url":"https://api.github.com/repos/Keck-DataReductionPipelines/MosfireDRP/issues/35","id":153104392,"user":{"login":"followthesheep","id":3268415,"avatar_url":"https://avatars.githubusercontent.com/u/3268415?v=3","gravatar_id":"","url":"https://api.github.com/users/followthesheep","html_url":"https://github.com/followthesheep","followers_url":"https://api.github.com/users/followthesheep/followers","following_url":"https://api.github.com/users/followthesheep/following{/other_user}","gists_url":"https://api.github.com/users/followthesheep/gists{/gist_id}","starred_url":"https://api.github.com/users/followthesheep/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/followthesheep/subscriptions","organizations_url":"https://api.github.com/users/followthesheep/orgs","repos_url":"https://api.github.com/users/followthesheep/repos","events_url":"https://api.github.com/users/followthesheep/events{/privacy}","received_events_url":"https://api.github.com/users/followthesheep/received_events","type":"User","site_admin":false},"created_at":"2015-11-02T18:07:27Z","updated_at":"2015-11-02T18:07:27Z","body":"Hi Marc,\r\nHave you used this code to make a more recent bad pixel mask? Maybe we can compare the differences with the new pixel mask?\r\n\r\nHave you guys had a chance to look at the code in the rectification stage or in the stacking process? I think we still need to track down whether these steps are improperly propagating the bad pixels. \r\n\r\nThanks,\r\nTuan"}}